Systems and methods for sample preparation using sonication

ABSTRACT

Devices, systems and methods including a sonicator for sample preparation are provided. A sonicator may be used to mix, resuspend, aerosolize, disperse, disintegrate, or de-gas a solution. A sonicator may be used to disrupt a cell, such as a pathogen cell in a sample. Sample preparation may include exposing pathogen-identifying material by sonication to detect, identify, or measure pathogens. A sonicator may transfer ultrasonic energy to the sample solution by contacting its tip to an exterior wall of a vessel containing the sample. Multipurpose devices including a sonicator also include further components for additional actions and assays. Devices, and systems comprising such devices, may communicate with a laboratory or other devices in a system for sample assay and analysis. Methods utilizing such devices and systems are provided. The improved sample preparation devices, systems and methods are useful for analyzing samples, e.g. for diagnosing patients suffering from infection by pathogens.

CROSS-REFERENCE TO RELATED APPLICATION

This application is a divisional of, and claims priority under 35 U.S.C.§ 120 to, U.S. patent application Ser. No. 14/203,436, filed Mar. 10,2014, which claims priority under 35 U.S.C. § 119(e) to U.S. PatentApplication Ser. No. 61/799,533, filed Mar. 15, 2013.

BACKGROUND

Rapid and accurate detection and identification of pathogens such asbacteria is important, and can be critical, in the diagnosis andtreatment of infectious diseases, and in the prevention or ameliorationof pandemics or epidemics. However, methods for detecting or identifyingpathogens often require large samples, which can be difficult to obtain,or may be uncomfortable or painful for the subject. Methods fordetecting or identifying pathogens often require the incubation ofsamples on growth media, or in host cells or animals, and so take longperiods of time. Many pathogens are difficult to culture, or are similarto other organisms, and so are difficult to identify even if the sampleyields a detectable culture. In addition, methods for detecting oridentifying pathogens may require rare or expensive reagents or cultureconditions.

Thus, detection and identification of pathogens in a biological samplemay be important in the diagnosis and treatment of patients exposed to,or suspected of suffering, from infectious diseases. However, presentmethods for detecting or identifying pathogens are often inaccurate,difficult, expensive, and time-consuming. Accordingly, rapid, accurateand straightforward methods for the detection and identification ofpathogens from small samples are desired.

INCORPORATION BY REFERENCE

All publications, patents, and patent applications mentioned in thisspecification are herein incorporated by reference to the same extent asif each individual publication, patent, or patent application wasspecifically and individually indicated to be incorporated by reference.

SUMMARY

Devices, systems and methods for sample preparation are disclosed.Devices for sample preparation as disclosed herein comprise a sonicator;the sonicator may be configured to provide ultrasonic energy to a samplesolution. A sample solution may be contained within a vessel. Inembodiments, a sonicator may be used to mix a solution, e.g., to mix asample solution, or to mix two or more solutions, such as a samplesolution and a reagent solution. In embodiments, a sonicator may be usedfor emulsification of a solution or a mixture of solutions, or of asample in a solution or reagent. In embodiments, a sonicator may be usedfor resuspension of a material, e.g., resuspension of a sample followingcentrifugation of the sample. In embodiments, a sonicator may be usedfor aerosolization of a liquid, e.g., aerosolization of a liquid sample,or of a solution comprising a sample. In embodiments, a sonicator may beused to heat a solution, such as a sample, or a solution comprising asample. In embodiments, a sonicator may be used for dispersing a sample,or a sample in a solution, or other material, such as, e.g., dispersinga solid or semi-solid sample in a solution. In embodiments, a sonicatormay be used to disintegrate a material, such as a sample, e.g., a solidor semi-solid sample may be exposed to sonication for disintegration,which may aid in its subsequent mixing into a reagent such as a diluent.In embodiments, a sonicator may be used to de-gas a liquid, such as afluid sample; in embodiments, gas released in this way may become betteravailable for assay. In embodiments, a sonicator may be used to disrupta cell, such as a pathogen cell in a sample.

Pathogens may be detected and identified by their characteristic geneticmaterial and characteristic proteins. Detection and identification ofpathogens in a biological sample typically requires disruption of thepathogen to expose its nuclear material to testing, and to provide moreaccessible proteins and protein/membrane complexes for assay.Pathogen-identifying material may be released from the pathogen bydisruption, e.g., by disruption of a pathogen membrane or cell wall. Forexample, disruption of the plasma membrane of any cell, or of a nuclearmembrane of a eukaryotic pathogen, or disruption of the cell wall of abacterium having a cell wall, or a combination of the same, may beeffective to free pathogen-identifying material (e.g., DNA, RNA, orprotein) for contact with assay reagents for detection, identification,or measurement.

Devices, systems and methods for disrupting pathogens in a biologicalsample are provided. Devices, systems and methods for disruptingpathogens in a biological sample as disclosed herein comprise asonicator; the sonicator may be configured to provide ultrasonic energyto a sample solution containing a pathogen effective to disrupt thepathogen, e.g., to disrupt a membrane of the pathogen. Such disruptionmay be effective to release pathogen-identifying material from thepathogen, aiding in the detection, identification, or measurement of thepathogen. In embodiments, multipurpose devices are provided whichinclude a sonicator configured to disrupt pathogen cells in a biologicalsample, exposing pathogen-identifying material for assay. Multipurposedevices are provided which include a sonicator configured to disruptpathogen cells in a biological sample, exposing pathogen-identifyingmaterial for assay, and which may also perform at least one additionalassay are provided. Systems comprising such devices are provided.Systems comprising such devices may further communicate with alaboratory or with other devices in a system for the detection andidentification of pathogens, and for diagnosis of infectious diseases.Methods utilizing such devices and systems are provided. The devices,systems and methods disclosed herein provide advantages useful fordiagnosing and treating patients suspected of, or suffering from,infection by pathogens. A biological sample may comprise blood, urine,sputum, tears, material obtained from a nasal swab, throat swab, cheekswab, or other sample obtained from a subject.

Applicants disclose devices configured to assay a biological sample forthe presence of pathogen-identifying material, said devices comprising asonicator, said sonicator being configured to contact a vesselcontaining said biological sample. Such a sonicator may be configuredfor use in the performance of said assay. A sonicator in a device asdisclosed herein may be configured to contact a wall of a vesselcontaining at least a portion of a biological sample, effective toprovide ultrasonic energy to said wall, effective to disrupt a pathogenin said biological sample and to release pathogen-identifying materialfrom said pathogen. An assay may comprise detection ofpathogen-identifying material; an assay may comprise identification ofpathogen-identifying material; an assay may comprise measuringpathogen-identifying material, e.g., measuring an amount ofpathogen-identifying material in a sample or portion of a sample. Suchpathogen-identifying material may be detected, or may be identified, ormay be measured, in an assay performed with said biological sample. Inembodiments, a device disclosed herein may be configured to perform oneor more other assay in addition to an assay directed to the detection,identification, or measurement of pathogen-identifying material.

A device as disclosed herein may be suitable for detection,identification, or measurement of pathogen-identifying material in abiological sample. In embodiments, a device for assaying a sample forthe presence of pathogen-identifying material in a sample may comprise asonicator, wherein said sonicator comprises means for contacting a wallof a vessel containing at least a portion of a biological sample. Inembodiments, a device for assaying a sample for the presence ofpathogen-identifying material in a sample may comprise: a sonicator; ansample handling system for transporting at least a portion of abiological sample; a vessel holder effective to hold a vessel having awall; and a detector effective to detect or measure pathogen-identifyingmaterial (e.g., an optical detector). In embodiments, a sonicator maycomprise a tip; in embodiments, a sonicator tip may be effective tocontact said vessel wall and to transfer ultrasonic energy to saidvessel wall from said sonicator. In embodiments, a sonicator maycomprise a sonicator horn, which horn may have a tip, and said horn andtip may be effective to contact said vessel wall and to transferultrasonic energy to said vessel wall from said sonicator. Inembodiments, a device may further comprise a communication assembly,which may comprise a display element or a communication elementeffective to report the results of said detection and/or measurement. Inembodiments, a communication assembly, such as a display element and/orcommunication element, may be suitable for two-way communication.

In embodiments, a device for assaying a sample for the presence ofpathogen-identifying material in a sample may comprise a sonicator,wherein said sonicator comprises means for contacting a wall of a vesselcontaining at least a portion of a biological sample. In embodiments, adevice for assaying a sample for the presence of pathogen-identifyingmaterial in a sample may comprise: a sonicator; sample handling systemmeans for transporting at least a portion of a biological sample; meansfor holding a vessel having a wall; means for contacting said vesselwall with at least a portion of said sonicator; and means for detecting,identifying, or measuring pathogen-identifying material (e.g., means fordetecting an optical signal, and/or measuring an optical property of thecombined composition with sample). In embodiments, a device may furthercomprise means for displaying or reporting the results of said detectionand/or measurement. In embodiments, a sonicator may comprise a tipmeans, which may comprise a sonicator horn, configured to make effectivecontact with a surface, such as a vessel wall, effective to transferultrasonic energy from said sonicator to said surface. In furtherembodiments, a device for assaying a sample for the presence ofpathogen-identifying material in a sample may comprise one or more of:detection means (e.g., an optical detector) for detecting the target;display means; and communication means for reporting the results of saiddetection and/or measurement. In embodiments, display means and/orcommunication means may be suitable for two-way communication.

Applicants further disclose systems comprising a device as disclosedherein. In embodiments, a system as disclosed herein may be used todetect the presence of, identify, or measure the amount of,pathogen-identifying material in a sample.

Applicants disclose herein systems for detecting the presence ofpathogen-identifying material in a biological sample, e.g., a sample ofblood, urine, sputum, tears, material from a nasal swab, throat swab,cheek swab, or other sample obtained from a subject. In embodiments, asystem for detecting the presence of pathogen-identifying material in asample may comprise a device as disclosed herein, and a means forcommunicating information from said device to a computer, a computernetwork, a telephone, a telephone network, or a device configured todisplay information communicated from said device.

Applicants disclose herein systems for identifying pathogen-identifyingmaterial in a biological sample, e.g., a sample of blood, urine, sputum,tears, material from a nasal swab, throat swab, cheek swab, or othersample obtained from a subject. In embodiments, a system for identifyingpathogen-identifying material in a sample may comprise a device asdisclosed herein, and a means for communicating information from saiddevice to a computer, a computer network, a telephone, a telephonenetwork, or a device configured to display information communicated fromsaid device.

Applicants disclose herein systems for measuring the amount ofpathogen-identifying material in a biological sample, e.g. a sample ofblood, urine, sputum, tears, material from a nasal swab, throat swab,cheek swab, or other sample obtained from a subject. In embodiments, asystem for measuring the amount of pathogen-identifying material in asample may comprise a device as disclosed herein, and a means forcommunicating information from said device to a computer, a computernetwork, a telephone, a telephone network, or a device configured todisplay information communicated from said device.

It will be understood that a means for communicating information mayinclude means for one-way communication and may include means fortwo-way communication, and may include means for communication withmultiple locations or entities. In embodiments, a system for detectingthe presence of pathogen-identifying material in a sample, a system foridentifying pathogen-identifying material in a sample, and a system formeasuring the amount of pathogen-identifying material in a sample, maycomprise a device as disclosed herein, and a communication assembly,which may comprise a channel for communicating information from saiddevice to a computer, said wherein said channel is selected from acomputer network, a telephone network, a metal communication link, anoptical communication link, and a wireless communication link. It willbe understood that a communication assembly, e.g., comprising a channelfor communicating information, may comprise a one-way communicationchannel and may be a two-way communication channel, and may comprisechannels for communication with multiple locations or entities.

The methods disclosed herein may be performed on a device, or on asystem, for processing a sample as disclosed herein. The methodsdisclosed herein can be readily incorporated into and used in anautomated assay device, and in an automated assay system, as disclosedherein. For example, systems as disclosed herein may include acommunication assembly for transmitting or receiving a protocol based onthe analyte to be detected (e.g., pathogen-identifying material) orbased on other analytes to be detected by the device or system. Inembodiments, an assay protocol may be changed based on optimalscheduling of a plurality of assays to be performed by a device, or maybe changed based on results previously obtained from a sample from asubject, or based on results previously obtained from a different samplefrom the subject. In embodiments, a communication assembly may comprisea channel for communicating information from said device to a computer,said wherein said channel is selected from a computer network, atelephone network, a metal communication link, an optical communicationlink, and a wireless communication link. In embodiments, systems asdisclosed herein may transmit signals to a central location, or to anend user, and may include a communication assembly for transmitting suchsignals. Systems as disclosed herein may be configured for updating aprotocol as needed or on a regular basis.

Accordingly, Applicants disclose devices configured to detect, identify,or measure pathogen-identifying material in a biological sample, e.g.,of blood, urine, sputum, material obtained from a nasal swab, a throatswab, a cheek swab, or other sample. Such detection, identification, ormeasurements may be made according to a method disclosed herein. Devicesconfigured to detect, identify, or measure pathogen-identifying materialin a biological sample, e.g., of blood, urine, sputum, material obtainedfrom a nasal swab, a throat swab, a cheek swab, or other sample,according to a method disclosed herein may be configured to determinepathogen-identifying material from a biological sample that comprises nomore than about 1000 μL of a biological sample, or no more than about500 μL of a biological sample, or no more than about 250 μL of abiological sample, or no more than about 150 μL of a biological sample,or no more than about 100 μL of a biological sample, or no more thanabout 50 μL of a biological sample, or, in embodiments, wherein saidsample of blood comprises no more than about 25 μL of a biologicalsample, or wherein said sample of blood comprises no more than about 10μL of a biological sample, or wherein said sample of blood comprisesless than about 10 μL of a biological sample. Such devices may beconfigured to detect, identify, or measure pathogen-identifying materialin a biological sample, e.g., of blood, urine, sputum, material obtainedfrom a nasal swab, a throat swab, a cheek swab, or other sample, in lessthan about one hour, or, in embodiments, in less than about 40 minutes,or in less than about 30 minutes, or in less than about 20 minutes, orless than about 10 minutes, or less than about 5 minutes, or less.

Devices disclosed herein may be configured to perform an assay for thedetection, identification, or measurement of pathogen-identifyingmaterial, and also to perform an assay for the measurement of anotheranalyte in the biological sample, e.g., of blood, urine, sputum,material obtained from a nasal swab, a throat swab, a cheek swab, orother sample. Devices disclosed herein may be configured to perform anassay for the detection, identification, or measurement ofpathogen-identifying material, and also to perform an assay comprisingmeasurement of a morphological characteristic of a blood cell in thebiological sample, e.g., of blood, urine, sputum, material obtained froma nasal swab, a throat swab, a cheek swab, or other sample. Devicesdisclosed herein may be configured to perform an assay for thedetection, identification, or measurement of pathogen-identifyingmaterial, and also to perform an assay comprising measurement of anotheranalyte, e.g., a vitamin, a hormone, a drug or metabolite of a drug, orother analyte. Such devices may be configured wherein the assays, or theorder of performance of assays, that are performed by said device may bealtered by communication with another device.

Applicants also disclose systems comprising a device as disclosedherein. In embodiments, the system comprises a device that is configuredto perform an assay for the measurement of pathogen-identifying materialand also to perform an assay for the measurement of another analyte inthe biological sample, e.g., of blood, urine, sputum, material obtainedfrom a nasal swab, a throat swab, a cheek swab, or other sample. Inembodiments, the system comprises a device that is configured to performan assay for the measurement of pathogen-identifying material and alsoto perform an assay for the measurement of a morphologicalcharacteristic of a blood cell in the biological sample, e.g., of blood,urine, sputum, material obtained from a nasal swab, a throat swab, acheek swab, or other sample. In embodiments of such a system, assays, orthe order of performance of assays, that are performed by said devicemay be altered by communication with another device.

Applicants disclose herein a method of disrupting a pathogen in abiological sample, comprising: transporting at least a portion of abiological sample to a vessel, said vessel having an interior portionand an exterior wall, effective to place said portion of said biologicalsample into said interior portion of said vessel; contacting an exteriorwall of said vessel containing said biological sample with a sonicator;and applying ultrasound energy to said wall of the vessel effective todisrupt a target pathogen in said biological sample. In embodiments,such transporting of at least a portion of a biological sample to avessel may comprise transporting by sample handling system.

Applicants disclose herein a method of detecting the presence ofpathogen-identifying material in a biological sample, comprising:transporting at least a portion of a biological sample to a vessel, saidvessel having an interior portion and an exterior wall, effective toplace said portion of said biological sample into said interior portionof said vessel; contacting an exterior wall of said vessel containingsaid biological sample with a sonicator; applying ultrasound energy tosaid wall of the vessel effective to release pathogen-identifyingmaterial from a target pathogen in said biological sample; and detectingthe presence of pathogen-identifying material. In embodiments, suchtransporting of at least a portion of a biological sample to a vesselmay comprise transporting at least a portion of a biological sample by asample handling system.

Applicants disclose herein a method of identifying a pathogen in abiological sample, comprising: transporting at least a portion of abiological sample to a vessel, said vessel having an interior portionand an exterior wall, effective to place said portion of said biologicalsample into said interior portion of said vessel; contacting an exteriorwall of said vessel containing said biological sample with a sonicator;applying ultrasound energy to said wall of the vessel effective todisrupt a target pathogen in said biological sample; and identifying apathogen in the sample. In embodiments, such transporting of at least aportion of a biological sample to a vessel may comprise transporting atleast a portion of a biological sample by a sample handling system.

Applicants disclose herein a method of measuring the amount ofpathogen-identifying material in a biological sample, comprising:transporting at least a portion of a biological sample to a vessel, saidvessel having an interior portion and an exterior wall, effective toplace said portion of said biological sample into said interior portionof said vessel; contacting an exterior wall of said vessel containingsaid biological sample with a sonicator; applying ultrasound energy tosaid wall of the vessel effective to release pathogen-identifyingmaterial from a target pathogen in said biological sample; and measuringthe amount of pathogen-identifying material. In embodiments, suchtransporting of at least a portion of a biological sample to a vesselmay comprise transporting at least a portion of a biological sample by asample handling system.

Applicants disclose herein devices and systems comprising a sonicator,and methods using such device and systems to detect, identify, ormeasure pathogens in a sample by detecting, identifying, or measuringpathogen-identifying material released in a sample as a result ofdisruption caused by application of ultrasonic energy to the sample. Asdisclosed herein, ultrasonic energy may be applied to a sample by directcontact between the sample and a sonicator (e.g., between a sample and atip portion of a sonicator); by indirect contact between a sample and asonicator, wherein the sonicator contacts a compliant barrier that is incontact with a sample; by indirect contact between a sample and asonicator, wherein the sonicator contacts a wall of a vessel containinga sample; or by other means. Ultrasonic energy suitable for disruptingpathogens using devices, systems, and methods as disclosed hereinincludes ultrasonic energy between about 20 kiloHertz (kHz) and about 60kHz; between about 20 kHz and about 50 kHz; between about 20 kHz andabout 40 kHz; or between about 20 kHz and about 30 kHz. Ultrasonicenergy suitable for disrupting pathogens using devise, systems, andmethods as disclosed herein includes ultrasonic energy at or about 20kHz; at or about 25 kHz; at or about 28 kHz; at or about 30 kHz; at orabout 35 kHz; at or about 40 kHz; at or about 45 kHz; at or about 50kHz; at or about 55 kHz; or at or about 60 kHz.

In embodiments, pathogen-identifying material may comprise a nucleicacid, and may comprise a pathogen-identifying sequence of nucleic acids.In embodiments, pathogen-identifying material may comprise an aminoacid, and may comprise a pathogen-identifying sequence of amino acids.In embodiments, detecting the presence of pathogen-identifying materialcomprises contacting said pathogen-identifying material with a probe,which may be a labeled probe. In embodiments, a probe, including alabeled probe, may comprise nucleic acids. In embodiments, a probe,including a labeled probe, may comprise a sequence of nucleic acidscomplementary to at least a portion of said pathogen-identifyingmaterial. In embodiments, a probe, including a labeled probe, maycomprise amino acids. In embodiments, a probe, including a labeledprobe, may comprise an antibody or an antibody fragment whichspecifically binds to at least a portion of said pathogen-identifyingmaterial.

In embodiments, a probe, or a complex, may comprise a label. Inembodiments, a label may be selected from the group consisting of a dye,an epitope tag, a fluorescent moiety, a luminescent moiety, achemiluminescent moiety, an enzymatic label, a magnetic label, aparamagnetic label, a contrast agent, a nanoparticle, a radioisotope,biotin, streptavidin, and a quencher.

In embodiments, detecting the presence of pathogen-identifying materialmay comprise detecting a complex comprising pathogen-identifyingmaterial, or detecting a probe bound to pathogen-identifying material insaid sample. In embodiments of the methods disclosed herein, a detectingstep may comprise detecting the presence of a label.

In embodiments, identifying a pathogen-identifying material may compriseidentifying a complex comprising pathogen-identifying material, ordetecting a probe bound to pathogen-identifying material in said sample.In embodiments of the methods disclosed herein, an identifying step maycomprise detecting the presence of a label.

In embodiments, measuring the amount of pathogen-identifying materialmay comprise measuring the amount of a complex comprisingpathogen-identifying material, or measuring the amount of probe bound topathogen-identifying material in said sample. In embodiments of themethods disclosed herein, a measuring step may comprise measuring theamount of probe, or label, bound or released, may comprise measuring alabel or measuring the amount of a label.

In embodiments of the methods disclosed herein, detecting probe bound topathogen-identifying material may comprise an optical measurement,identifying pathogen-identifying material may comprise an opticalmeasurement, and measuring the amount of probe bound may comprise anoptical measurement. In embodiments, optical measurement may comprisedetection of, or measurement of, the intensity of electromagneticradiation passing through, or emitted from, a composition comprisingsaid biological sample.

Methods, devices, and systems disclosed herein provide rapid assayswhich require only small amounts of sample, such as only small amountsof blood. Device and systems disclosed herein are configured to performsuch rapid assays which require only small amounts of sample, such asonly small amounts of blood, urine, sputum, tears, material obtainedfrom a nasal swab, throat swab, cheek swab, or other biological sample.Accordingly, the methods, devices, and systems provide rapid tests,which require only small biological samples, and thus provide advantagesover other methods, compositions, assays, devices, and systems.

This Summary is provided to introduce a selection of concepts in asimplified form that are further described below in the DetailedDescription. This Summary is not intended to identify key features oressential features of the claimed subject matter, nor is it intended tobe used to limit the scope of the claimed subject matter.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 presents a schematic illustration of an embodiment of a system asdisclosed herein, including a sonicator having a sonicator horn, avessel configured to hold a sample, a vessel holder configured to hold avessel for sonication, a sample handling system configured to place asample within a vessel, a detector for detecting pathogen-identifyingmaterial from a sample, a communications assembly (labeled communicationlink/display), which may comprise a display, for receiving instructionsand information, and for providing information and data to a user, or toother components or equipment, a controller to operate the components ofthe system, and a power supply to enable the operation of thecomponents.

FIG. 2 shows an example of a sonicator suitable for an embodiment of thedevices, systems, and methods disclosed herein. In embodiments, aportion of the tip of a sonicator may touch or be inserted into a samplesolution in a vessel. In such embodiments, the sonicator tip contactsthe sample solution. In an embodiment of configurations illustrated inthis figure, the tip portion of the sonicator may be prevented fromcontacting the sample by the interposition of a compliant barriermaterial (e.g., the vessel may have a compliant covering, such as acompliant plastic or rubber covering). Pressing the sonicator tip onto aproximal side of the compliant barrier, effective to cause a distalportion of the compliant barrier to contact the solution within thevessel, allows transfer of ultrasonic energy from the sonicator to thesample solution in the vessel while preventing direct contact betweenthe sonicator tip and the sample solution.

FIG. 3 shows an example of a sonicator suitable for an embodiment of thedevices, systems, and methods disclosed herein, in which a portion ofthe sonicator contacts a wall of the vessel holding a sample solution;in such embodiments, no portion of the sonicator contacts the samplesolution, preventing contamination of the sample and of the sonicator,so that there is no requirement to clean or condition the sonicator tipbefore its re-use.

FIG. 4 shows an example of an embodiment of a sonicator having a colletfor holding a vessel. The collet may be cinched around a vesselcontained within the collet to provide a tight fit between the colletand vessel; such a tight fit may aid in the efficient transfer ofultrasonic energy between the transducer of the sonicator (via thecollet) and the vessel.

FIG. 5 shows an example of a sonicator mounted for use in an embodimentof the devices disclosed herein. As shown, a distal portion of thesonicator passes through a port in a vessel holder, allowing directcontact between the sonicator and a wall of a vessel held by the vesselholder. As shown, a vessel holder may have a further aperture, allowingaccess to another portion of the vessel, and including optical accesswithout requiring an optical path through a wall of the vessel holder.As shown, a vessel holder may have walls without apertures; such wallsmay be configured for optical access as well, by construction usingsuitable materials; by providing a wall of proper flatness, orientation,or thickness of the wall; by proper preparation or construction of thewall surface, or by other means.

FIGS. 6A and 6B provide views of an embodiment of a sonicator andsonicator assembly suitable for devices, systems, and methods asdisclosed herein. FIG. 6A shows a side view of an embodiment of asonicator mounted with a solenoid configured to move the sonicator hornin a transverse direction (e.g., towards the vessel holder, or away fromthe vessel holder, as shown in the figure). A spring is provided to urgethe sonicator away from the vessel holder upon release of solenoid forcedrawing the sonicator towards the vessel holder. The sonicator horn isdisposed so as to approach a vessel held within the vessel holder. Atrest (with the solenoid off), as shown in FIG. 6A, the sonicator horndoes not contact a vessel held within the vessel holder, and the springis in an extended conformation.

FIG. 6B shows a side view of an embodiment of a sonicator mounted with asolenoid configured to move the sonicator horn in a transverse direction(e.g., towards the vessel holder, or away from the vessel holder, asshown in the figure). A spring is provided to urge the sonicator awayfrom the vessel holder upon release of solenoid force drawing thesonicator towards the vessel holder. The sonicator horn is disposed soas to approach a vessel held within the vessel holder. With the solenoidon, as shown in FIG. 6B, the sonicator horn is in contact with an outerwall of a vessel held within the vessel holder, and the spring is in acompressed conformation. Operation of the sonicator in thisconfiguration, in which the sonicator horn is in contact with a wall ofa vessel held within the vessel holder, is effective to provideultrasonic energy to a sample solution within the vessel. Providingsufficient ultrasonic energy for s sufficient amount of time iseffective to disrupt cells within the sample solution; in particular,pathogen cells within the sample solution may be disrupted, effective torelease pathogen-identifying material for detection, identification, andmeasurement.

FIG. 7 provides a further example of a solenoid assembly suitable foruse in the devices and systems disclosed herein. In this figure, thevessel is covered with a cap; such a cap is effective to prevent loss ofsample fluid during sonication, and to prevent spread of sample contents(by spillage, aerosolization, or other means) outside the vessel. Inthis figure, a vessel is shown held in a vessel holder, and a sonicatorhorn is shown in contact with a side wall of the vessel. Such aconfiguration is an operative configuration effective to disrupt cellswithin the sample solution, such as pathogen cells within the samplesolution.

FIG. 8 provides a schematic illustration of a device having a sonicatorand other features as disclosed herein. The device illustrated by thefigure has a sonicator with a sonicator horn, which can be made tocontact a wall of a vessel (e.g., by motion of a movable sonicatormount, as indicated in the figure). The vessel can contain a samplesolution, and is configured to be held by a vessel holder. As shown, avessel cap may be disposed on a surface of the vessel. A sample handlingsystem may be provided effective to transport a biological sample, or aportion thereof, and reagents if applicable, to the vessel. As discussedherein, a sample handling system may also be configured to manipulate ormove a vessel, a vessel cap, or other article, within a housing of adevice. A device may have a detector, e.g., within the device housing asillustrated in the figure, such as a detector configured to detectpathogen-identifying materials released by sonication of a samplesolution. A device may further include other components for performingassays, detecting analytes, and collecting and communicating dataobtained from biological samples.

FIG. 9 provides a schematic diagram of an embodiment of a portion of adevice having multiple, multiplexed sonicators. In a device comprisingmultiple sonicators, such sonicators and the associated multiplexer,power supply, cabling, controller, and other associated components aretypically placed within the housing of a device. In a system comprisingmultiple sonicators, which may not all be in the same device, suchsonicators and the associated multiplexer, power supply, cabling,controller, and other associated components are typically placed withinseparate housings, e.g., within the housings of the correspondingdevices of the system.

FIGS. 10A-10D provide examples of embodiments of vessels suitable forcontaining a sample solution for sonication. FIG. 10A shows a side viewof a vessel, with a flat wall surface facing outward, and the opening(for filling the vessel) shown at the top. The bottom of the vesselshown is also flat; the flat side wall and the flat bottom areconfigured to contact a tip portion of a sonicator, such as a tip of asonicator horn. The wider portion at the top of the vessel includessurfaces and mating sockets. The mating sockets comprise recessesconfigured for engagement of a transport and/or force-providing member(e.g., a nozzle of a sample handling system) which a) allows transportof the vessel and b) provides a surface for provision of downward forceto oppose upward force of a sonicator horn placed on a flat bottomsurface of the vessel. FIG. 10B shows a side view of a vessel as shownin FIG. 10A, with a flat wall surface facing rightward, and the opening(for filling the vessel) shown at the top. FIG. 10C shows a vessel asshown in FIGS. 10A and 10B, with a flat wall surface facing leftward andslightly upward, and the opening (for filling the vessel) shown at thetop. Openings of the mating sockets are visible in this view, as is aninner ridge within the internal chamber of the vessel. An inner ridge asillustrated in the figure may be configured to seat, or to seal, a cap.FIG. 10D shows a cross-sectional view of a vessel as shown in FIGS.10A-C, with the opening (for filling the vessel) shown at the top. Theridge and inner chamber of the vessel, and the shape and depth of themating sockets are visible in this cross-sectional view.

FIGS. 11A-11D provide further embodiments of vessels suitable forcontaining a sample solution for sonication. FIG. 11A shows anembodiment of a tubular vessel with a rounded bottom. FIG. 11B shows anembodiment of a conical vessel with a rounded bottom. FIG. 11C anembodiment of an elongated tubular vessel with a rounded bottom. FIG.11D shows an embodiment of a wide tubular vessel with a rounded bottom.

FIGS. 12A-12D provide yet further embodiments of vessels suitable forcontaining a sample solution for sonication. FIG. 12A shows anembodiment of a tubular vessel with a rounded bottom and a tapered(e.g., partially conical-shaped cap). FIG. 12B shows an embodiment of aconical vessel with a rounded bottom having flat side surfacesconfigured to engage with a sonicator tip. FIG. 12C an embodiment of anelongated tubular vessel with a rounded bottom and a protruding flatsurface configured to engage with a sonicator tip. FIG. 12D shows anembodiment of a wide tubular vessel with a rounded bottom having a capconnected to the vessel via cap linkage.

FIG. 13 illustrates a configuration in which a vessel having a flatbottom is disposed to contact a tip of a sonicator. Such contact iseffective to transfer ultrasonic energy to the wall of the vessel andthereby to a sample solution contained within the vessel, effective todisrupt cells in the sample solution when the sonicator is activated.Functional contact between the vessel and the sonicator may be aided orimproved by the spring shown in the figure. (Note that the action andfunction of the spring in this figure is opposite to that of the springsshown in FIGS. 6A, 6B, and 7. The present spring acts to urge thesonicator and vessel together; the springs shown in FIGS. 6A, 6B, and 7act to urge the sonicator and vessel apart from each other.) Functionalcontact between the vessel and the sonicator may be aided or improved byapplication of force (as illustrated by the downward arrow in thefigure) urging the vessel onto the tip of the sonicator horn, improvingfunctional contact and improving energy transfer from the sonicator tothe sample solution and cells within it.

FIG. 14 presents the results of quantitative polymerase chain reaction(qPCR) measurements made from pathogen-identifying material released forassay by sonication according to the present methods. The horizontalaxis represents the number of cycles while the vertical axis (inrelative light units) represents the numbers of copies of the targetnucleic acid sequence indicative of the target pathogen. As shown in thefigure, all target nucleic acids were detectable after about 25 cycles.

DETAILED DESCRIPTION

Applicants provide devices, systems, and methods for disrupting cellsusing a sonicator. Sonicators provide ultrasonic energy which disruptscells by producing, for example, cavitation within a sample fluidcontaining the cells, which cells may be disrupted by sonoporation dueto cavitation in the fluid. In embodiments, such devices, systems, andmethods for disrupting cells using a sonicator may be applied to anexternal surface of a vessel, where the vessel contains a biologicalsample suspected of harboring a pathogen or multiple pathogens. Asonicator may provide ultrasonic energy to a vessel, for example, bycontacting a wall of the vessel with its tip portion (e.g., with a tipof a sonicator horn), effective to transfer energy through the vesselwall to fluid within the vessel. Such fluid may comprise a biologicalsample. Applicants further disclose vessels for use with sonicators asdisclosed herein and with devices and systems comprising suchsonicators.

Accordingly, embodiments of devices and systems for detecting,identifying, or measuring pathogen-identifying material in at least aportion of a biological sample, e.g., of blood, urine, sputum, materialobtained from a nasal swab, a throat swab, a cheek swab, or othersample; and embodiments of devices and systems for detecting,identifying, or measuring pathogen-identifying material in at least aportion of a biological sample, e.g., of blood, urine, sputum, materialobtained from a nasal swab, a throat swab, a cheek swab, or othersample, and at least one other biologically relevant attribute from saidbiological sample, e.g., of blood, urine, sputum, material obtained froma nasal swab, a throat swab, a cheek swab, or other sample, from asubject are disclosed herein.

Devices, systems, and methods disclosed herein may comprise, and may beused with, devices, systems, and methods as disclosed in, for example,U.S. Pat. Nos. 8,088,593; 8,380,541; U.S. patent application Ser. No.13/769,798, filed Feb. 18, 2013; U.S. patent application Ser. No.13/769,779, filed Feb. 18, 2013; U.S. patent application Ser. No.13/244,947 filed Sep. 26, 2011; PCT/US2012/57155, filed Sep. 25, 2012;U.S. application Ser. No. 13/244,946, filed Sep. 26, 2011; U.S. patentapplication Ser. No. 13/244,949, filed Sep. 26, 2011; and U.S.Application Ser. No. 61/673,245, filed Sep. 26, 2011, the disclosures ofwhich patents and patent applications are all hereby incorporated byreference in their entireties.

Devices disclosed herein comprise a sonicator configured to transferultrasonic energy to a sample solution. In embodiments, a sonicator,e.g., a sonicator tip, may contact a sample solution directly. Inembodiments, a sonicator, e.g., a sonicator tip, may contact a samplesolution indirectly via a barrier material. In embodiments, a barriermaterial may be a compliant material. In embodiments, a sonicator, e.g.,a sonicator tip, may not contact a sample solution directly, but mayinstead be configured to contact a wall or other surface of a vesselcontaining a solution to which ultrasonic energy is to be directed.

A sonicator may comprise a sonicator horn, e.g., may comprise anelongated portion configured to transmit and/or concentrate ultrasonicenergy at a small area distal from the oscillator of the sonicator. Asonicator (and its sonicator horn) may have a tip configured to contactand to interact with a vessel containing a solution to which ultrasonicenergy is to be directed. In embodiments, a sonicator may be mounted ona sonicator mount, which may be configured to hold a sonicator in anoperating position during use. In embodiments, a sonicator may bemounted on a sonicator mount, which may be configured to place asonicator in a disengaged position when not in use transmittingultrasonic energy.

In embodiments, a sonicator mount may provide for movement of thesonicator, e.g., may allow the engagement and disengagement of thesonicator with a vessel wall, as needed for the operation of thesonicator. For example, a device comprising a sonicator may include asonicator mount operably connected with a solenoid configured to place asonicator tip in contact with a vessel containing a sample solution whenthe solenoid is activated, where the sonicator is mounted effective thatthe sonicator tip is removed from contact with the vessel when thesolenoid is not activated. In embodiments, a spring may be used to aidin removing a sonicator tip from contact with a vessel when a solenoidis not activated.

In embodiments, a sample solution may be contained in a vessel, and aportion of a sonicator may be applied to an external wall of the vessel.In embodiments, the external wall to which a sonicator is applied may bea side wall of the vessel. In embodiments, the external wall to which asonicator is applied may be a bottom wall of the vessel. In embodiments,the external wall to which a sonicator may be applied is a top wall ofthe vessel. In embodiments, a sonicator may be applied to more than onewall of the vessel.

A vessel comprises an internal chamber configured for holding fluid,such as a sample solution (although it will be understood that such aninternal chamber may hold a reagent, or water, or any other fluid). Avessel will typically include an opening configured to accept a samplesolution; for example, a vessel may be filled (partially or completely)via an opening. Where the vessel has only a single opening leading to aninner chamber, that opening defines the top of the vessel. Inembodiments, the vessel is open to the environment, e.g., has an openpassage at its top. In embodiments, a vessel may be configured to accepta cap, where the cap is effective to occlude an opening in the vessel,e.g., to close an open passage at the top of the vessel. In embodiments,a cap may be a separate element (e.g., may be able to be completelyseparated from the vessel); in embodiments, a cap may be a portion of avessel capable of moving into and out of a position that occludes anopening or passage that (when not occluded) provides access to aninterior portion of the vessel. In embodiments, a cap may comprise aportion of a vessel. For example, a cap may be connected to otherportions of a vessel by a hinge, or by a thread, or cable, or otherflexible connector of any kind. In embodiments, the vessel is closed,and not open to the environment, when ultrasonic energy is applied toit. A cap, when in place occluding an opening of a vessel, may beeffective to prevent or reduce spilling of a sample solution held withinthe vessel. A cap, when in place occluding an opening of a vessel, maybe effective to prevent or reduce loss of sample solution due tosplashing, bubble formation, aerosolization, or other actions due todelivery of ultrasonic energy to a sample solution held within thevessel.

In embodiments of the devices, systems and methods disclosed herein, asample handling system may be used to transport and deliver a samplesolution to a vessel, and to fill a vessel (either partially or fully)with a sample solution. In embodiments, a sample handling systemcomprises a pipette. A pipette may be configured to accept a pipettetip, e.g., to mount and transport a pipette tip attached to the pipette.In embodiments, a pipette comprises a nozzle configured to accept apipette tip. A pipette may be configured to aspirate a fluid, such as asample solution, into a pipette tip attached to the pipette (e.g., apipette tip which is attached to a nozzle of the pipette). Inembodiments, a pipette may be configured to dispense a fluid, such as asample solution, from a pipette tip attached to the pipette (e.g., to anozzle of the pipette). A pipette may be configured to transmit force toa surface or component of a device. In embodiments, a pipette nozzle maycontact a surface or component of a device, effective to transmit forceto that surface or component. In embodiments, a pipette nozzle maycontact a mating recess of a vessel, and, in embodiments, may engage amating recess of a vessel. In embodiments, two, or more pipette nozzlesmay contact mating recesses of a vessel, and, in embodiments, may engagemating recesses of a vessel. In embodiments, a pipette of a samplehandling system may be movable, and is preferably movable in at leasttwo, and more preferably in three dimensions (e.g., is movable in one,two, or all three of horizontally, laterally, and vertically).

In embodiments, devices comprising a sonicator, and systems and methodscomprising or using such devices, may comprise a detector configured todetect pathogen-identifying material in a sample. A detector may be, forexample, an optical detector, such as a spectrophotometer, aphotomultiplier, a charge-coupled device, a camera, or other device orsystem configured to detect a light-based signal indicative of thepresence of a pathogen-identifying material. In embodiments, a detectormay be configured to, or be effective to, detect a signal comprisingchemiluminescence, luminescence, fluorescence, absorbance,transmittance, turbidity, a color change, or other change in light,whether emitted, transmitted, or absorbed, effective to signal thepresence of a pathogen-identifying material in a sample. In embodiments,a detector may comprise an electrochemical detector, or a temperaturesensor, or a pH sensor, or a radiation sensor, or an ion-sensitiveelectrode, or other sensor capable of detecting the presence of apathogen-identifying material in a sample.

Methods for detecting pathogen-identifying material include assays fordetecting nucleic acids (e.g., DNA or RNA), assays for detectingpeptides and proteins (including glycoproteins), assays for detectingother pathogen-related molecules, complement fixation assays,hemagglutination assays (e.g., for influenza), and other assays. Methodsfor detecting nucleic acids include polymerase chain reaction (PCR)methods (including quantitative PCR (qPCR), reverse-transcriptase PCD(RT-PCR), “real-time” PCR, one-step PCR, two-step PCR, and other methodsknown in the art. Methods for detecting peptides and proteins includeenzyme immunoassays such as Enzyme-Linked ImmunoSorbent Assays (ELISAs)and other assays utilizing antibodies or antibody fragments,complement-based reactions, measurement of absorbance of ultraviolet orother frequency of light, assays utilizing specific receptor-ligandinteractions, and other assays known in the art. Assays for detectingother pathogen-related molecules include assays for bacterial sugars andlipids (e.g., bacterial lipopolysaccharide (LPS)), and other assaysknown in the art. A detector for use with such assays may be an opticaldetector, a pH detector, an electrochemical detector, a temperaturesensor, an ion-sensitive electrode, a radiation detector, or otherdetector.

In embodiments, devices comprising a sonicator, and systems and methodscomprising or using such devices, may comprise a controller. Inembodiments, a controller may comprise a processor. In embodiments, acontroller may be connected to, and may control the operation of,components of a device; such components are typically disposed within ahousing of the device. In embodiments, a controller may control theoperation of a sonicator. In embodiments, a controller may control theoperation of a sample handling system. In embodiments, a controller maycontrol the operation of a detector. In embodiments, a controller maycontrol the operation of any component or unit of the device. Othercomponents may include, for example, a camera, a chemistry assay unit, anucleic acid assay unit, a heating unit, a communication unit, a proteinchemistry unit, or other component or unit. In embodiments, a controllermay control the operation of one or more components of a deviceaccording to a protocol. In embodiments, a protocol by which acontroller controls the operation of any one or more component or unitof a device may be preprogrammed, e.g., may be resident on the device.In embodiments, a protocol by which a controller controls the operationof any one or more component or unit of a device may be obtained fromanother device, or from a user, or from a laboratory, or from a network,or from the cloud. In embodiments, a protocol by which a controllercontrols the operation of any one or more component or unit of a devicemay be updated, or may be updatable, according to information orinstructions from another device, or from a user, or from a laboratory,or from a network, or from the cloud. In embodiments, a device mayreceive information, or instructions, or updates, or protocols, via auser interface. In embodiments, a device may receive information, orinstructions, or updates, or protocols, via a communication assembly.

In embodiments, devices comprising a sonicator, and systems and methodscomprising or using such devices, may comprise a display effective toprovide a user with information regarding the operation of the device,information regarding the progress of an assay performed by the device,or information regarding the results of an assay performed by thedevice. In embodiments, a display may comprise a visual display, or maycomprise a printed display, or may comprise an audio signal, which mayinclude an audio signal understandable as speech by a user, or maycomprise any combination or all of such displays. In embodiments, adisplay may comprise a user interface. In embodiments in which a displaycomprises a user interface, a device may receive, e.g., information,commands, protocols, or other input.

In embodiments, devices comprising a sonicator, and systems and methodscomprising or using such devices, may comprise a communication assemblyeffective to communicate with one or more of a user, another device, alaboratory, a network, the cloud, or other communication target. Inembodiments, a communication assembly may provide a communication targetwith information regarding the operation of the device, informationregarding the progress of an assay performed by the device, orinformation regarding the results of an assay performed by the device.In embodiments, a communication assembly may be configured to allow adevice to receive, e.g., information, commands, protocols, or otherinput from an outside source, such as, e.g., a user, another device, alaboratory, a network, the cloud, or other communication source.

Definitions

Before the present devices, systems, and methods are disclosed anddescribed, it is to be understood that the terminology used herein isfor the purpose of describing particular embodiments only and is notintended to be limiting. It is also to be understood that the presentdisclosure provides explanatory and exemplary descriptions and examples,so that, unless otherwise indicated, the devices, systems, and methodsdisclosed herein are not limited to the specific embodiments describedherein.

It must be noted that, as used in the specification and the appendedclaims, the singular forms “a,” “an” and “the” include plural referentsunless the context clearly dictates otherwise. Thus, for example,reference to “a salt” refers to a single salt or mixtures of differentsalts, and the like.

In this specification and in the claims that follow, reference will bemade to a number of terms, which shall be defined to have the followingmeanings:

Acronyms and abbreviations, such as “rpm” (revolutions per minute),“min” (minute), “sec” (second), and so forth, have their customarymeanings.

As sued herein, the term “assay” and grammatical equivalents refers totests, measurements, observations, and other experimental procedureswhich may be applied to a sample for detection of an analyte,identification of an analyte, and measurement of the amounts of ananalyte in a sample. Assays may be physical assays which detect,identify, or measure a physical property of a sample; assays may bechemical assays, which detect, identify, or measure a chemical propertyof a sample, or perform chemical reactions in or with a sample; andinclude assays which use optical, electrical or electronic, chemical, orother means of detection and measurement.

As used herein the term “ultrasound” refers to vibrations at frequenciesbeyond those capable of being detected by a human subject, i.e.,frequencies greater than about 20,000 cycles per second (20 kiloHerz(kHz)).

As used herein the term “ultrasonic energy” refers to the energy ofvibrations at frequencies beyond those capable of being detected by ahuman subject, i.e., frequencies greater than about 20,000 cycles persecond (20 kHz). A sonicator may be effective to produce and applyultrasonic energy.

As used herein, the term “sonicator” refers to a device effective toprovide ultrasonic energy, e.g., by providing mechanical energy,typically in the form of vibrations, at ultrasonic frequencies. Asonicator may include a driving element which provides high-frequencyvibrations; for example, many sonicators utilize piezoelectric materialsto produce high-frequency vibrations. Piezoelectric ultrasoundgenerators typically require high voltages (e.g., about 200 volts (V) toabout 400 V) to provide the needed alternating current drive to operatesuch generators.

As sonicator has a tip portion, which includes the distal tip andportions nearby; ultrasonic energy from a sonicator is typicallytransmitted to a target material by the tip portion. Sonicators oftenhave sonicator horns, often made from stainless steel, for example,configured to direct ultrasonic energy to a tip portion; where asonicator has a sonicator horn, the tip of the sonicator horn comprisesthe sonicator tip, and the tip portion of the sonicator horn comprisesthe sonicator tip portion.

As used herein, the terms “horn” and “sonicator horn” refer to a portionof a sonicator configured to focus ultrasonic energy, or to provide apathway for the direction of ultrasonic energy, to a destination. A hornmay be designed and configured to transfer or transmit ultrasonic energyin an efficient manner, and may, for example, be configured to resonateat particular frequencies which may be tuned or adapted to particularfrequencies of choice of a driving element of a sonicator. A horn mayhave a tip, or tip portion; a horn tip or tip portion may be configuredto maximize energy transfer, e.g., by maximizing contact, to a vessel,or wall of a vessel, or to a fluid contained within a vessel.

As used herein, the terms “fill” and “filled” and their grammaticalequivalents, e.g., as used in phrases such as “a vessel may be filledwith a sample solution” refer to the transfer of any amount, includingpartial filling and complete filling. These terms as used herein do notrequire that such filling completely fill a container, but include anylesser amount of filling as well.

As used herein, the terms “detect”, “detection”, “detecting” andgrammatical equivalents refer to a determination that a target analyte,such as a pathogen-identifying material, is present. Detection does notrequire that a minimum amount of the target analyte be present in thesample, but merely that the analyte be observed to be present, whetherdirectly or indirectly (although in practical terms, a lower limit belowwhich detection is unlikely to occur may exist).

As used herein, the terms “identify”, “identification”, “identifying”,and grammatical equivalents refer to a determination of the identity ofa target analyte found in a sample. Such identification, in addition todetection, may be useful where detection may be ambiguous as to thespecific identity of a detected analyte; for example, where an influenzavirus is detected, it may further be useful to identify the particularstrain, or strains, of influenza found in the sample. Thus,identification may provide more detailed and specific information thandoes detection.

As used herein, the terms “measure”, “measurement”, “measuring”, andgrammatical equivalents refer to a determination of the amounts of atarget analyte found in a sample. Thus, measurement providesquantitative information which may not be provided by detection oridentification, or which may be more precise that information providedby detection or identification.

The term “nucleic acid” refers to nucleotides and nucleosides which makeup, for example, deoxyribonucleic acid (DNA) macromolecules andribonucleic acid (RNA) macromolecules. Nucleic acids may be identifiedby the base attached to the sugar (e.g., deoxyribose or ribose); nucleicacid sequences may be used to identify an organism from which thenucleic acid sequence was obtained.

The terms “polypeptide” and “protein” may be used interchangeably torefer to molecules comprised of amino acids linked by peptide bonds.Individual amino acids may be termed “residues” of a polypeptide orprotein. Unique amino acid sequences of polypeptides may be used toidentify the organisms from which the polypeptides were obtained.

The term “antibody” is used in the broadest sense and specificallycovers single monoclonal antibodies (including agonist and antagonistantibodies), antibody compositions with polyepitopic specificity, andantibody fragments. Monoclonal antibodies are obtained from a populationof substantially homogeneous antibodies, i.e., the individual antibodiescomprising the population are identical except for possiblenaturally-occurring mutations that may be present in minor amounts. Forexample, monoclonal antibodies may be made by the hybridoma method firstdescribed by Kohler et al., Nature, 256:495 (1975), or may be made byrecombinant DNA methods (see, e.g., U.S. Pat. No. 4,816,567 to Cabillyet al.).

“Antibody fragment”, and all grammatical variants thereof, as usedherein is defined as a (1) portion of an intact antibody comprising theantigen binding site or variable region of the intact antibody, whereinthe portion is free of the constant heavy chain domains (i.e. CH2, CH3,and CH4, depending on antibody isotype) of the Fc region of the intactantibody, and (2) constructs comprising a portion of an intact antibody(as defined by the amino acid sequence of the intact antibody)comprising the antigen binding site or variable region of the intactantibody. Examples of antibody fragments include Fab, Fab′, Fab′-SH,F(ab′)₂, Fd, Fc, Fv, diabodies, and any other “Non-single-chainantigen-binding unit” as described, e.g., in U.S. Pat. No. 7,429,652.

The term “pathogen” as used herein refers to an agent that may cause adisease, such as an infectious disease, in a subject. Pathogens include,for example, Gram-negative bacteria, Gram-positive bacteria, otherbacteria, RNA viruses, DNA viruses, prions, yeast, fungi, protozoans,helminths, nematodes, and any other pathogenic agent which may sicken asubject or, if transmitted from a subject who may not suffer disease,could cause disease in a further subject to which the pathogen istransmitted.

As used herein, “pathogen-identifying material” refers to proteins andnucleic acids derived from a pathogen, such as a bacterium, a prion, avirus, a yeast cell, a fungus, a protozoan (also termed “protist”), ahelminth, nematode, or other viral, single cellular or multicellularorganism which may be found in a biological sample collected from asubject. Pathogen-identifying material may comprise a target nucleicacid. Pathogen-identifying material may comprise a target peptide, orepitope (e.g., a portion of a peptide). The proteins, and the nuclearmaterial of such organisms (whether DNA or RNA), is indicative of theparticular type of organism, and may be used to detect the presence ofsuch an organism, and to identify it. Quantitative measurements ofpathogen-identifying material provide measurements of the amounts ofsuch organisms in a biological sample, and may be used to determine theseverity of an infection, or to track the progress of a disease, and totrack the course and success of its treatment.

The term “probe” as used herein refers to a material which is useful toidentify a target compound or cell; a probe may be, e.g., a nucleic acidprobe, a protein probe, or other probe. A target compound may beproduced by, or found in or on, a prion, a virus, a bacterium, a yeast,a fungus, a protozoan, or other pathogen. A probe, as used herein, maycomprise RNA or DNA, or analogs of RNA or DNA, effective that the probemay recognize and bind (e.g., hybridize) to a target nucleic acid. Atarget nucleic acid may be, e.g., a viral, bacterial, yeast, fungal,protozoan, helminth, nematode, or other nucleic acid sequence (which maybe a portion of a longer nucleic acid sequence). A probe, as usedherein, may comprise a polypeptide or protein, such as an antibody orantibody fragment, which may recognize and bind to a target compound orportion of a compound (e.g., an epitope of a protein that is indicativeof a target pathogen).

As used herein, a “marker”, a “label”, a “label” and a “label moiety”refer to a detectable compound or composition which is conjugateddirectly or indirectly to the antibody so as to generate a “labeled”antibody. A label or marker provides a detectable signal for at leastthe time period during which a signal is to be observed. The label ormarker may be detectable by itself (e.g. radioisotope labels orfluorescent labels) or, in the case of an enzymatic label, may catalyzechemical alteration of a substrate compound or composition which isdetectable.

A marker or label may be linked (non-covalently or covalently) to anucleic acid probe, an antibody or antibody fragment, or other probe. Alabel may alter its detectability (e.g., become detectable, or increase,or decrease its detectability) upon contact with its target. A label maydetach from its probe upon contact between the probe and its target, andthus may alter its detectability. Such alterations in detectability areuseful in assays for detecting, identifying, or measuring analytes in asample.

A label may be, for example, a dye, an epitope tag, a fluorescentmoiety, a luminescent moiety, a chemiluminescent moiety, an enzymaticlabel, a magnetic label, a paramagnetic label, a contrast agent, ananoparticle, a radioisotope, biotin, streptavidin, and a quencher. Ananoparticle may be a particle of an element, such as a goldnanoparticle, or of an alloy or compound, such as a quantum dot (aparticle of a semiconductor material), or other particle having a sizetypically in a range between about 1 nm to about 100 nm.

As used herein, the terms “sample” and “biological sample” refer to ablood, urine, sputum, tears, material from a nasal swab, throat swab,cheek swab, or other bodily fluid, excretion, secretion, or tissueobtained from a subject. These terms are inclusive of an entire sampleand of a portion of a sample. As used herein, reference to a fluidsample includes reference to a sample and a biological sample. Suchsamples may include fluids into which material has been deposited, wheresuch material may be obtained from a nasal swab, throat swab, cheekswab, or other sample which may include solid or semi-solid material,whether along with or without natural fluids. Such fluids and samplescomprise fluid samples and sample solutions.

As used herein the “sample solution” refers to a fluid sample itself,and to dilutions, mixtures, aliquots, or other solutions which containat least a portion of a sample.

As used herein the terms “sample handling system”, “fluid handlingsystem” and grammatical equivalents refer to systems configured toobtain, transport, and deliver fluids. In embodiments disclosed herein,such systems comprise pipettes, nozzles, pipette tips, mechanicalcomponents configured to move a pipette, a nozzle, or a pipette tip to adesired location. Such a desired location is typically within a housingof a device. In embodiments, a pipette tip may be mounted on a nozzle;in embodiments, a pipette tip may be removably mounted on a nozzle,effective that a nozzle may engage and mount a first pipette tip, usethe first pipette tip, discard the first pipette tip, and then engageand mount a second pipette tip. Such systems comprise means foraspirating liquid into a pipette tip. Such systems comprise means fordispensing liquid from a pipette tip. In embodiments of such systems, apipette and nozzle may engage and mount an element other than a pipettetip; for example, in embodiments disclosed herein, a pipette and nozzlemay engage and mate with a mating socket of a vessel (see, e.g., FIGS.10 and 11). In embodiments, a pipette and nozzle mated with a matingsocket of a vessel may be used to transport the vessel to a desiredlocation within a device. In embodiments, a pipette and nozzle matedwith a mating socket of a vessel may be used to apply force to a vessel(see, e.g., FIG. 11 for a configuration where such application of forcemay be useful).

The methods disclosed herein can be readily incorporated into and usedin device for processing a sample, or a system for processing a sample,which may be an automated assay device, or may be an automated assaysystem. Such assay devices and assay systems may comprise devices andsystems disclosed, for example, in U.S. Pat. Nos. 8,088,593; 8,380,541;U.S. patent application Ser. No. 13/769,798, filed Feb. 18, 2013; U.S.patent application Ser. No. 13/769,779, filed Feb. 18, 2013; U.S. patentapplication Ser. No. 13/244,947 filed Sep. 26, 2011; PCT/US2012/57155,filed Sep. 25, 2012; U.S. application Ser. No. 13/244,946, filed Sep.26, 2011; U.S. patent application Ser. No. 13/244,949, filed Sep. 26,2011; and U.S. Application Ser. No. 61/673,245, filed Sep. 26, 2011, thedisclosures of which patents and patent applications are all herebyincorporated by reference in their entireties.

Such a device, and such a system, may be useful for the practice of themethods disclosed herein. For example, a device may be useful forreceiving a sample. A device may be useful for preparing, or forprocessing a sample. A device may be useful for performing an assay on asample. A device may be useful for obtaining data from a sample. Adevice may be useful for transmitting data obtained from a sample. Adevice may be useful for disposing of a sample following processing orassaying of a sample.

A device may be part of a system, a component of which may be a sampleprocessing device. A device may be a sample processing device. A sampleprocessing device may be configured to facilitate collection of asample, prepare a sample for a clinical test, or effect a chemicalreaction with one or more reagents or other chemical or physicalprocessing, as disclosed herein. A sample processing device may beconfigured to obtain data from a sample. A sample processing device maybe configured to transmit data obtained from a sample. A sampleprocessing device may be configured to analyze data from a sample. Asample processing device may be configured to communicate with anotherdevice, or a laboratory, or an individual affiliated with a laboratory,to analyze data obtained from a sample.

A sample processing device may be configured to be placed in or on asubject. A sample processing device may be configured to accept a samplefrom a subject, either directly or indirectly. A sample may be, forexample, a biological sample, e.g., of blood, urine, sputum, materialobtained from a nasal swab, a throat swab, a cheek swab, or othersample, (e.g., a sample obtained from a fingerstick, or fromvenipuncture, or an arterial biological sample, e.g., of blood, urine,sputum, material obtained from a nasal swab, a throat swab, a cheekswab, or other sample,), a urine sample, a biopsy sample, a tissueslice, stool sample, or other biological sample; a water sample, a soilsample, a food sample, an air sample; or other sample. A biologicalsample, e.g., of blood, urine, sputum, material obtained from a nasalswab, a throat swab, a cheek swab, or other sample, may comprise, e.g.,whole blood, plasma, or serum. A sample processing device may receive asample from the subject through a housing of the device. The samplecollection may occur at a sample collection site, or elsewhere. Thesample may be provided to the device at a sample collection site.

In some embodiments, a sample processing device may be configured toaccept or hold a cartridge. In some embodiments, a sample processingdevice may comprise a cartridge. The cartridge may be removable from thesample processing device. In some embodiments, a sample may be providedto the cartridge of the sample processing device. Alternatively, asample may be provided to another portion of a sample processing device.The cartridge and/or device may comprise a sample collection unit thatmay be configured to accept a sample.

A cartridge may include a sample, and may include reagents for use inprocessing or testing a sample, disposables for use in processing ortesting a sample, or other materials. Following placement of a cartridgeon, or insertion of a cartridge into, a sample processing device, one ormore components of the cartridge may be brought into fluid communicationwith other components of the sample processing device. For example, if asample is collected at a cartridge, the sample may be transferred toother portions of the sample processing device. Similarly, if one ormore reagents are provided on a cartridge, the reagents may betransferred to other portions of the sample processing device, or othercomponents of the sample processing device may be brought to thereagents. In some embodiments, the reagents or components of a cartridgemay remain on-board the cartridge. In some embodiments, no fluidics areincluded that require tubing or that require maintenance (e.g., manualor automated maintenance).

A sample or reagent may be transferred to a device, such as a sampleprocessing device. A sample or reagent may be transferred within adevice. Such transfer of sample or reagent may be accomplished withoutproviding a continuous fluid pathway from cartridge to device. Suchtransfer of sample or reagent may be accomplished without providing acontinuous fluid pathway within a device. In embodiments, such transferof sample or reagent may be accomplished by a sample handling system(e.g., a pipette); for example, a sample, reagent, or aliquot thereofmay be aspirated into an open-tipped transfer component, such as apipette tip, which may be operably connected to a sample handling systemwhich transfers the tip, with the sample, reagent, or aliquot thereofcontained within the tip, to a location on or within the sampleprocessing device. The sample, reagent, or aliquot thereof can bedeposited at a location on or within the sample processing device.Sample and reagent, or multiple reagents, may be mixed using a samplehandling system in a similar manner. One or more components of thecartridge may be transferred in an automated fashion to other portionsof the sample processing device, and vice versa.

A device, such as a sample processing device, may have a fluid handlingsystem (also termed herein a sample handling system). A fluid handlingsystem may perform, or may aid in performing, transport, dilution,extraction, aliquotting, mixing, and other actions with a fluid, such asa sample. In some embodiments, a fluid handling system may be containedwithin a device housing. A fluid handling system may permit thecollection, delivery, processing and/or transport of a fluid,dissolution of dry reagents, mixing of liquid and/or dry reagents with aliquid, as well as collection, delivery, processing and/or transport ofnon-fluidic components, samples, or materials. The fluid may be asample, a reagent, diluent, wash, dye, or any other fluid that may beused by the device, and may include, but not limited to, homogenousfluids, different liquids, emulsions, suspensions, and other fluids. Afluid handling system, including without limitation a pipette, may alsobe used to transport vessels (with or without fluid contained therein)around the device. The fluid handling system may dispense or aspirate afluid. The sample may include one or more particulate or solid matterfloating within a fluid.

In embodiments, a fluid handling system may comprise a pipette, pipettetip, syringe, capillary, or other component. The fluid handling systemmay have portion with an interior surface and an exterior surface and anopen end. The fluid handling system may comprise a pipette, which mayinclude a pipette body and a pipette nozzle, and may comprise a pipettetip. A pipette tip may or may not be removable from a pipette nozzle. Inembodiments, a fluid handling system may use a pipette mated with apipette tip; a pipette tip may be disposable. A tip may form afluid-tight seal when mated with a pipette. A pipette tip may be usedonce, twice, or more times. In embodiments, a fluid handling system mayuse a pipette or similar device, with or without a pipette tip, toaspirate, dispense, mix, transport, or otherwise handle the fluid. Thefluid may be dispensed from the fluid handling system when desired. Thefluid may be contained within a pipette tip prior to being dispensed,e.g., from an orifice in the pipette tip. In embodiments, or instancesduring use, all of the fluid may be dispensed; in other embodiments, orinstances during use, a portion of the fluid within a tip may bedispensed. A pipette may selectively aspirate a fluid. The pipette mayaspirate a selected amount of fluid. The pipette may be capable ofactuating stirring mechanisms to mix the fluid within the tip or withina vessel. The pipette may incorporate tips or vessels creatingcontinuous flow loops for mixing, including of materials or reagentsthat are in non-liquid form. A pipette tip may also facilitate mixtureby metered delivery of multiple fluids simultaneously or in sequence,such as in 2-part substrate reactions.

A fluid handling system may include one or more fluidically isolated orhydraulically independent units. For example, the fluid handling systemmay include one, two, or more pipette tips. The pipette tips may beconfigured to accept and confine a fluid. The tips may be fluidicallyisolated from or hydraulically independent of one another. The fluidcontained within each tip may be fluidically isolated or hydraulicallyindependent from one fluids in other tips and from other fluids withinthe device. The fluidically isolated or hydraulically independent unitsmay be movable relative to other portions of the device and/or oneanother. The fluidically isolated or hydraulically independent units maybe individually movable. A fluid handling system may comprise one ormore base or support. A base or support may support one or more pipetteor pipette units. A base or support may connect one or more pipettes ofthe fluid handling system to one another.

A sample processing device may be configured to perform processing stepsor actions on a sample obtained from a subject. Sample processing mayinclude sample preparation, including, e.g., sample dilution, divisionof a sample into aliquots, extraction, contact with a reagent,filtration, separation, centrifugation, or other preparatory orprocessing action or step. A sample processing device may be configuredto perform one or more sample preparation action or step on the sample.Optionally, a sample may be prepared for a chemical reaction and/orphysical processing step. A sample preparation action or step mayinclude one or more of the following: centrifugation, separation,filtration, dilution, enriching, purification, precipitation,incubation, pipetting, transport, chromatography, cell lysis, cytometry,pulverization, grinding, activation, ultrasonication, micro columnprocessing, processing with magnetic beads, processing withnanoparticles, or other sample preparation action or steps. For example,sample preparation may include one or more step to separate blood intoserum and/or particulate fractions, or to separate any other sample intovarious components. Sample preparation may include one or more step todilute and/or concentrate a sample, such as a biological sample, e.g.,of blood, urine, sputum, material obtained from a nasal swab, a throatswab, a cheek swab, or other sample, or other biological samples. Samplepreparation may include adding an anti-coagulant or other ingredients toa sample. Sample preparation may also include purification of a sample.In embodiments, all sample processing, preparation, or assay actions orsteps are performed by a single device. In embodiments, all sampleprocessing, preparation, or assay actions or steps are performed withina housing of a single device. In embodiments, most sample processing,preparation, or assay actions or steps are performed by a single device,and may be performed within a housing of a single device. Inembodiments, many sample processing, preparation, or assay actions orsteps are performed by a single device, and may be performed within ahousing of a single device. In embodiments, sample processing,preparation, or assay actions or steps may be performed by more than onedevice.

A sample processing device may be configured to run one or more assay ona sample, and to obtain data from the sample. An assay may include oneor more physical or chemical treatments, and may include running one ormore chemical or physical reactions. A sample processing device may beconfigured to perform one, two or more assays on a small sample ofbodily fluid. One or more chemical reaction may take place on a samplehaving a volume, as described elsewhere herein. For example one or morechemical reaction may take place in a pill having less than femtolitervolumes. In an instance, the sample collection unit is configured toreceive a volume of the bodily fluid sample equivalent to a single dropor less of blood or interstitial fluid. In embodiments, the volume of asample may be a small volume, where a small volume may be a volume thatis less than about 1000 μL, or less than about 500 μL, or less thanabout 250 μL, or less than about 150 μL, or less than about 100 μL, orless than about 75 μL, or less than about 50 μL, or less than about 40μL, or less than about 20 μL, or less than about 10 μL, or other smallvolume. In embodiments, all sample assay actions or steps are performedon a single sample. In embodiments, all sample assay actions or stepsare performed by a single device. In embodiments, all sample assayactions or steps are performed within a housing of a single device. Inembodiments, most sample assay actions or steps are performed by asingle device, and may be performed within a housing of a single device.In embodiments, many sample assay actions or steps are performed by asingle device, and may be performed within a housing of a single device.In embodiments, sample processing, preparation, or assay actions orsteps may be performed by more than one device.

A sample processing device may be configured to perform a plurality ofassays on a sample. For example, a sample processing device may beconfigured to detect, or to identify, or to measure pathogen-identifyingmaterial in a sample. In embodiments, a sample processing device may beconfigured to perform a plurality of assays on a single sample. Inembodiments, a sample processing device may be configured to perform aplurality of assays on a single biological sample, where the biologicalsample is a small sample. For example, a small sample may have a samplevolume that is a small volume of less than about 1000 μL, or less thanabout 500 μL, or less than about 250 μL, or less than about 150 μL, orless than about 100 μL, or less than about 75 μL, or less than about 50μL, or less than about 40 μL, or less than about 20 μL, or less thanabout 10 μL, or other small volume. A sample processing device may becapable of performing multiplexed assays on a single sample. A pluralityof assays may be run simultaneously; may be run sequentially; or someassays may be run simultaneously while others are run sequentially. Oneor more control assays and/or calibrators (e.g., including aconfiguration with a control of a calibrator for the assay/tests) canalso be incorporated into the device; control assays and assay oncalibrators may be performed simultaneously with assays performed on asample, or may be performed before or after assays performed on asample, or any combination thereof. In embodiments, all sample assayactions or steps are performed by a single device. In embodiments, allof a plurality of assay actions or steps are performed within a housingof a single device. In embodiments, most sample assay actions or steps,of a plurality of assays, are performed by a single device, and may beperformed within a housing of a single device. In embodiments, manysample assay actions or steps, of a plurality of assays, are performedby a single device, and may be performed within a housing of a singledevice. In embodiments, sample processing, preparation, or assay actionsor steps may be performed by more than one device.

In embodiments, all of a plurality of assays may be performed in a shorttime period. In embodiments, such a short time period comprises lessthan about three hours, or less than about two hours, or less than aboutone hour, or less than about 40 minutes, or less than about 30 minutes,or less than about 25 minutes, or less than about 20 minutes, or lessthan about 15 minutes, or less than about 10 minutes, or less than about5 minutes, or less than about 4 minutes, or less than about 3 minutes,or less than about 2 minutes, or less than about 1 minute, or othershort time period.

A sample processing device may be configured to detect one or moresignals relating to the sample. A sample processing device may beconfigured to identify one or more properties of the sample. Forinstance, the sample processing device may be configured to detect thepresence or concentration of one analyte or a plurality of analytes or adisease condition in the sample (e.g., in or through a bodily fluid,secretion, tissue, or other sample). Alternatively, the sampleprocessing device may be configured to detect a signal or signals thatmay be analyzed to detect the presence or concentration of one or moreanalytes (which may be indicative of a disease condition) or a diseasecondition in the sample. The signals may be analyzed on board thedevice, or at another location. Running a clinical test may or may notinclude any analysis or comparison of data collected.

A chemical reaction or other processing step may be performed, with orwithout the sample. Examples of steps, tests, or assays that may beprepared or run by the device may include, but are not limited toimmunoassay, nucleic acid assay, receptor-based assay, cytometric assay,colorimetric assay, enzymatic assay, electrophoretic assay,electrochemical assay, spectroscopic assay, chromatographic assay,microscopic assay, topographic assay, calorimetric assay, turbidmetricassay, agglutination assay, radioisotope assay, viscometric assay,coagulation assay, clotting time assay, protein synthesis assay,histological assay, culture assay, osmolarity assay, and/or other typesof assays, centrifugation, separation, filtration, dilution, enriching,purification, precipitation, pulverization, incubation, pipetting,transport, cell lysis, or other sample preparation action or steps, orcombinations thereof. Steps, tests, or assays that may be prepared orrun by the device may include imaging, including microscopy, cytometry,and other techniques preparing or utilizing images. Steps, tests, orassays that may be prepared or run by the device may further include anassessment of histology, morphology, kinematics, dynamics, and/or stateof a sample, which may include such assessment for cells.

A device may be capable of performing all on-board steps (e.g., steps oractions performed by a single device) in a short amount of time. Adevice may be capable of performing all on-board steps on a singlesample in a short amount of time. For example, from sample collectionfrom a subject to transmitting data and/or to analysis may take about 3hours or less, 2 hours or less, 1 hour or less, 50 minutes or less, 45minutes or less, 40 minutes or less, 30 minutes or less, 20 minutes orless, 15 minutes or less, 10 minutes or less, 5 minutes or less, 4minutes or less, 3 minutes or less, 2 minutes or less, or 1 minute orless. The amount of time from accepting a sample within the device totransmitting data and/or to analysis from the device regarding such asample may depend on the type or number of steps, tests, or assaysperformed on the sample. The amount of time from accepting a samplewithin the device to transmitting data and/or to analysis from thedevice regarding such a sample may take about 3 hours or less, 2 hoursor less, 1 hour or less, 50 minutes or less, 45 minutes or less, 40minutes or less, 30 minutes or less, 20 minutes or less, 15 minutes orless, 10 minutes or less, 5 minutes or less, 4 minutes or less, 3minutes or less, 2 minutes or less, or 1 minute or less.

A device may be configured to prepare a sample for disposal, or todispose of a sample, such as a biological sample, following processingor assaying of a sample.

In embodiments, a sample processing device may be configured to transmitdata obtained from a sample. In embodiments, a sample processing devicemay be configured to communicate over a network. A sample processingdevice may include a communication assembly that may interface with thenetwork. A sample processing device may be connected to the network viaa wired connection or wirelessly. The network may be a local areanetwork (LAN) or a wide area network (WAN) such as the Internet. In someembodiments, the network may be a personal area network. The network mayinclude the cloud. The sample processing device may be connected to thenetwork without requiring an intermediary device, or an intermediarydevice may be required to connect a sample processing device to anetwork. A sample processing device may communicate over a network withanother device, which may be any type of networked device, including butnot limited to a personal computer, server computer, or laptop computer;personal digital assistants (PDAs) such as a Windows CE device; phonessuch as cellular phones, smartphones (e.g., iPhone, Android, Blackberry,etc.), or location-aware portable phones (such as GPS); a roamingdevice, such as a network-connected roaming device; a wireless devicesuch as a wireless email device or other device capable of communicatingwireless with a computer network; or any other type of network devicethat may communicate possibly over a network and handle electronictransactions. Such communication may include providing data to a cloudcomputing infrastructure or any other type of data storageinfrastructure which may be accessed by other devices.

A sample processing device may provide data regarding a sample to, e.g.,a health care professional, a health care professional location, such asa laboratory, or an affiliate thereof. One or more of a laboratory,health care professional, or subject may have a network device able toreceive or access data provided by the sample processing device. Asample processing device may be configured to provide data regarding asample to a database. A sample processing device may be configured toprovide data regarding a sample to an electronic medical records system,to a laboratory information system, to a laboratory automation system,or other system or software. A sample processing device may provide datain the form of a report.

A laboratory, device, or other entity or software may perform analysison data regarding a sample in real-time. A software system may performchemical analysis and/or pathological analysis, or these could bedistributed amongst combinations of lab, clinical, and specialty orexpert personnel. Analysis may include qualitative and/or quantitativeevaluation of a sample. Data analysis may include a subsequentqualitative and/or quantitative evaluation of a sample. Optionally, areport may be generated based on raw data, pre-processed data, oranalyzed data. Such a report may be prepared so as to maintainconfidentiality of the data obtained from the sample, the identity andother information regarding the subject from whom a sample was obtained,analysis of the data, and other confidential information. The reportand/or the data may be transmitted to a health care professional. Dataobtained by a sample processing device, or analysis of such data, orreports, may be provided to a database, an electronic medical recordssystem, to a laboratory information system, to a laboratory automationsystem, or other system or software.

Embodiments of the devices, systems, and methods disclosed herein arediscussed in the examples presented below.

EXAMPLES

The following examples disclose devices comprising a sonicator effectiveto disrupt pathogens in a biological sample.

Example 1 Systems for Disrupting Pathogens Comprising a Sonicator

Embodiments of systems disclosed herein include devices which have asonicator configured to apply ultrasonic energy to a sample solution.Application of ultrasonic energy to a sample solution containing apathogen may be effective to disrupt the pathogen and to releasepathogen-identifying material into the solution, where it can bedetected and the pathogen identified. In embodiments, the amounts ofpathogens present in the sample solution may be quantified followingapplication of ultrasonic energy effective to disrupt the pathogen andto release pathogen-identifying material into the solution. A schematicillustration representing elements of an embodiment of a systemcomprising devices having a sonicator is shown in FIG. 1

In embodiments, a tip portion of a sonicator of a device of a system asdisclosed herein be configured to improve the transfer of ultrasonicenergy to a sample solution, or to provide better contact between thesonicator and a vessel containing a sample solution, or both. Inembodiments, a sonicator of a device of a system as disclosed herein mayhave a sonicator horn; such a sonicator horn may have a tip portion,which may be configured to improve the transfer of ultrasonic energy toa sample solution, or to provide better contact between a sonicator anda vessel containing a sample solution, or both. In embodiments ofsystems disclosed herein, a system may include a vessel configured tohold a sample, and may include a vessel holder configured to hold avessel. A sample holder may be configured to place a vessel in a properposition for sonication; may be configured to hold a vessel duringsonication (in embodiments, such holding may comprise application offorce effective to restrain a vessel during sonication, e.g., to reduceloss of energy due to unwanted motion of a vessel, or for improvedenergy transfer during sonication); or may be configured to retain avessel in place until further operation is needed following sonication.

As shown in FIG. 1, in embodiments, a device of a system as disclosedherein may comprise a sample handling system configured to place asample within a vessel, by, for example, delivering at least a portionof a sample to a vessel and depositing the at least a portion into achamber of the vessel. A sample handling system may also be configuredto place a reagent, or other agent or material, within a vessel, by, forexample, delivering the reagent, other agent, or material, to a vesseland depositing it into a chamber of the vessel.

As shown in FIG. 1, in embodiments, a device of a system as disclosedherein may comprise a detector for detecting pathogen-identifyingmaterial from a sample. A detector may be any detector effective todetect the presence of pathogen-identifying material in a sample. Suchdetection may be aided by use of a label or other readily detectableagent, which may be used in conjunction with a reagent that specificallybinds to, or reacts with, a pathogen-identifying material.

As shown in FIG. 1, in embodiments, a system as disclosed herein maycomprise a controller to operate the components of the system. Inembodiments, a device of a system as disclosed herein may comprise acontroller to operate components of the device. A controller maycomprise a processor, or other component, device, or element effectiveto oversee and control the operation of a device. A controller mayfurther comprise communication components, devices, or elementseffective to provide communication with and between the controller andother components and elements of the device or system. Such internalcommunication linkages are illustrated in FIG. 1 by dotted lines. Itwill be understood that, in embodiments of the present devices andsystems, other communication linkages may also be provided.

In embodiments, a system as disclosed herein may comprise acommunication assembly, which may comprise one or more communicationslink(s). In embodiments, a device of a system as disclosed herein maycomprise a communication assembly, which may comprise one or morecommunications link(s). Such a communication assembly may comprise adisplay, for receiving instructions and information, and for providinginformation and data to a user, or to other components or equipment. Inembodiments, such a communication assembly may comprise a one-waycommunication link (e.g., from the device or system to a user, anotherdevice, a laboratory, a network, the cloud, or other communicationdestination; or to the device or system from a user, another device, alaboratory, a network, the cloud, or other communication source) and, inembodiments, may include a two-way (or multiple-way) communicationlink(s), e.g., between the device or system and a user, another device,a laboratory, a network, the cloud, or other communication targets. Suchcommunication links with communication destinations or sources areindicated by the dotted arrows in the figure.

In embodiments, a device or system as disclosed herein may comprise apower supply to enable the operation of the components. Powerconnections are illustrated in FIG. 1 by solid lines. It will beunderstood that, in embodiments of the present devices and systems,other power connections may also be provided.

As disclosed herein, ultrasonic energy may be applied to a sample bydirect contact between the sample and a sonicator (e.g., by immersion ofa sonicator tip or tip portion in a sample solution). As disclosedherein, ultrasonic energy may be applied indirectly to a sample, bycontacting a sonicator tip portion or tip with a material separating thesonicator tip and the sample solution, where the material is in contactboth with the sonicator tip portion or tip, and with the samplesolution. In embodiments comprising indirect contact, the materialseparating the sonicator and the solution may comprise a compliantbarrier. In embodiments comprising indirect contact, the materialseparating the sonicator and the solution may comprise a wall of avessel containing a sample. In any embodiment comprising indirectcontact, the material separating the sonicator and the solution isconfigured to transmit ultrasonic energy from the sonicator tip portionto the sample solution.

Example 2 Sonicators and Vessels

Examples of sonicators suitable for use in the present devices, systemsand methods are shown in FIG. 2 and FIG. 3. FIG. 2 may provide anillustration of an embodiment in which a distal portion of the sonicator(e.g., the tip of the sonicator horn), termed in this example the “tip”,contacts a sample solution in a vessel. In such embodiments, the tipcontacts the sample solution. Direct contact with the sample solutionprovides for direct transfer of energy from the sonicator to the samplesolution. However, such direct contact requires that the tip touch orenter into the sample solution, providing a possible source ofcontamination of the sample (and subsequent samples) and requiringcleaning steps and/or coating of the tip to reduce such contamination.

FIG. 2 may also provide an illustration of an embodiment in which thetip is separated from the sample solution by a compliant barrier (such acompliant barrier conforms, to a greater or lesser degree, to theoutline of the tip as the tip is pressed into a vessel towards asolution within the vessel). In such an embodiment, the tip contacts thebarrier, and the barrier contacts a sample solution in a vessel. In suchembodiments, the tip does not contact the sample solution, avoidingpossible problems which may arise due to direct contact with the samplesolution. Barrier materials tested include latex, nitrile, andpolyurethane barriers. However, a compliant barrier may break or becomeporous during use, and may absorb ultrasonic energy, reducing theefficiency of transferring ultrasonic energy from a tip to a solution.

An alternative embodiment is shown in FIG. 3, which shows an example inwhich a distal portion of the sonicator contacts a wall of the vesselholding a sample solution; in such embodiments, no portion of thesonicator contacts the sample solution, preventing contamination of thesample and of the sonicator, so that there is no requirement to clean orcondition the sonicator tip before its re-use. A wall of a vessel, whichmay be more rigid, and less compliant than a compliant barrier, may bemore efficient at transferring ultrasonic energy from a tip to asolution than a compliant barrier; for example, a rigid wall may absorbless energy than would be absorbed by a compliant barrier.

Although the contact between sonicator and sample solution is indirectin embodiments comprising the configuration illustrated in FIG. 3, ampleultrasonic energy is transferred via the wall of a vessel into a samplesolution contained therein, and cells, including pathogen cells, may be,and have been, disrupted in this way. Ultrasonic energy transfer fromsonicator to sample solution is improved in this configuration byproviding a flat surface on the vessel wall, as disclosed herein, whichis complementary to a flat surface on the sonicator tip. Transmission ofultrasonic energy in the configuration illustrated in FIG. 3 is improvedby tight contact between a sonicator tip and a wall of a vessel.Application of force between the vessel wall and the sonicator tip isalso helpful to provide effective ultrasonic energy transfer fromsonicator to sample solution.

Forces of between 1 newton (N) and 16 N have been examined. For example,experiments in which forces of 1, 2, 3, 4, 6, and 10 N were applied toforce contact between the tip of a sonicator horn and a polystyrene tuberesulted in effective disruption of a test pathogen. In theseexperiments, 332 μL of solution containing E. coli (ATCC 884) bacteriawas held in a polystyrene tube. A sonicator probe was applied to theouter wall of the polystyrene tube with 1, 2, 3, 4, 6, and 10 N of forceand ultrasonic energy was applied for 10 seconds. Such disruption wascomparable to that obtained with a commercial sonicator in which vialsare placed in wells in a block connected to an ultrasonic generator.However, the results with 1 N of contact force were variable, andconsidered inferior to the results obtained with the commercialsonicator. From the results of these and other experiments, it isbelieved that a contact force of between about 2 N to about 10 N, orbetween about 2 N to 6 N, or between about 3 N to about 5 N, or about 4N, is useful for providing effective transfer of ultrasonic energy fordisruption of pathogens by contacting a wall of a vessel containing asample solution.

Different materials exhibit different ultrasonic energy transfercharacteristics. For example, preferred vessel materials for ultrasonicenergy transfer through a vessel wall include polystyrene,polycarbonate, and polyethylene. Polystyrene was found to be a bettermaterial than polycarbonate and polyethylene; polycarbonate was found tobe a better material than polyethylene.

Ultrasonic disruption of pathogens may be performed with varyingfrequencies of ultrasonic energy. Higher frequencies allow for shortersonicator horns; conversely, sonicators designed to provide ultrasonicenergy at lower frequencies will have longer sonicator horns than dosonicators designed for higher frequencies. For example, ultrasonicfrequencies suitable for use in devices, systems and methods disclosedherein include ultrasonic frequencies of from about 20 kHz to about 60kHz, or from about 20 kHz to about 50 kHz, or from about 20 kHz to about40 kHz. In embodiments of the devices, systems and methods disclosedherein include ultrasonic frequencies devices, systems and methodsdisclosed herein, suitable ultrasonic frequencies include frequencies ofabout 20 kHz, about 25 kHz, about 28 kHz, about 30 kHz, about 35 kHz,about 40 kHz, about 45 kHz, about 50 kHz, about 55 kHz, and about 60kHz.

A sonicator may include or have attached to it multiple elements. FIG. 4shows an example of an embodiment of a sonicator having a transducer, amotor, a drawbar, and a collet. In embodiments, a motor may be effectiveto move (e.g., rotate) a drawbar connected to a collet at the tip of thesonicator. As shown in FIG. 4, such a sonicator may have a hollowsonicator horn; in the embodiment shown, the hollow sonicator hornencloses, and allows passage of, a drawbar which provides functionalconnection between a collet at the distal end of the sonicator andtransducer (and thus with the sonicator body as well). A drawbar such asthe drawbar shown in the figure that is connected to a collet and amotor may be used to cinch a collet around a vessel contained within thecollet to provide a tight fit between the collet and vessel; such atight fit may aid in the efficient transfer of ultrasonic energy betweenthe transducer of the sonicator (via the collet) and the vessel. Asshown in the figure, a sonicator having such a horn and drawbar may beconfigured to transfer ultrasonic energy from its proximal end (shownhere adjacent the motor, near the transducer) to its distal end(adjacent the collet). A collet such as the collet shown in the figuremay be configured to mate with and hold a vessel effective to provideultrasonic energy to a sample within a vessel. In embodiments, asonicator having such components at its tip may be configured totransfer ultrasonic energy to a sample solution, and in embodiments, maybe configured to transfer ultrasonic energy to a sample solution via avessel wall.

As shown in FIG. 5, a sonicator may be mounted on a movable mount foruse in an embodiment of the devices disclosed herein. The sonicatormount shown in FIG. 5 is operably connected to a solenoid, effectivethat when the solenoid is activated, the sonicator mount, and itsattached sonicator, are drawn towards the solenoid (in a distaldirection with reference to the sonicator). This motion moves thesonicator horn in the same (distal) direction, moving the tip of thesonicator horn deeper into the sonicator horn port of the vessel holder.When a vessel is in place within the vessel holder, activation of thesolenoid and the resulting movement presses the tip of the sonicatorhorn into contact with a side wall of the vessel. In embodiments, theaction of the solenoid generates a force at the area of contact betweenthe tip of the sonicator horn and the vessel wall. Such a force may be,for example, between about 2 N and about 10 N, or between about 2 N andabout 6 N, or preferably between about 3 N and about 5 N, or, inembodiments, about 4 N of force.

As shown, a vessel holder may have a further aperture, allowing accessto another portion of the vessel, and including optical access withoutpossible interference by the vessel holder. As shown, a vessel holdermay have walls without apertures; such walls may be configured foroptical access as well, by construction using suitable materials; byproviding a wall of proper flatness, orientation, or thickness of thewall; by proper preparation or construction of the wall surface, or byother means.

FIG. 6 provides further illustration of the design and operation of amovable sonicator operably connected to a solenoid for moving asonicator horn tip into functional contact with a wall of a vesselcontaining a sample solution. FIGS. 6A and 6B present a side view of anembodiment of a sonicator mounted and operably connected with a solenoidthat is configured to move the sonicator horn in a transverse direction.In FIG. 6A, the solenoid is not activated. FIG. 6A shows a side view ofan embodiment of a sonicator mounted with a solenoid configured to movethe sonicator horn in a transverse direction (e.g., leftwardly orrightwardly as shown in the figure). The oval encloses an area ofinterest, in which the sonicator horn tip moves to and contacts a vesselwall when a vessel is in place within the vessel holder. As shown, aspring is provided to urge the sonicator away from the vessel holderupon release of solenoid force drawing the sonicator towards the vesselholder. The sonicator horn is disposed so as to approach a vessel heldwithin the vessel holder when the sonicator is moved to the right in thefigure. At rest (with the solenoid off), as shown in FIG. 6A, thesonicator horn does not contact a vessel held within the vessel holder,and the spring is in an extended conformation.

The solenoid is activated in FIG. 6B, the sonicator horn is in contactwith an outer wall of a vessel held within the vessel holder, and thespring is in a compressed conformation. Operation of the sonicator inthis configuration, in which the sonicator horn is in contact with awall of a vessel held within the vessel holder, is effective to provideultrasonic energy to a sample solution within the vessel. Transfer ofultrasonic energy is improved by providing a firm contact between thesonicator horn tip and the vessel wall; as discussed above, ultrasonicenergy transfer is improved by providing transverse force (towards thevessel wall) of between about 2 N and about 10 N, or between about 2 Nand about 6 N, or about 3N to about 5N, or about 4 N of force. Providingsufficient ultrasonic energy for a sufficient amount of time iseffective to disrupt cells within the sample solution; in particular,pathogen cells within the sample solution may be disrupted, effective torelease pathogen-identifying material for detection, identification, andmeasurement.

FIG. 7 provides a further, more detailed illustration of contact betweensonicator horn tip and a vessel wall. The vessel is held in the vesselholder; in this example, the vessel has a vessel cap. In embodiments, avessel may be filled with a sample solution prior to placement of thevessel cap. In embodiments, a vessel may be filled with sample solutionthrough a vessel cap, e.g., by a conduit through the vessel cap. Such aconduit may be temporary (e.g., may be provided by a hollow needlepiercing the cap, where the path of the needle may reseal followingremoval of the needle from the cap). Such a conduit may be permanent,e.g., may be a channel or tube that is a permanent feature of the vesselcap. In embodiments, such a conduit may itself be capped. Inembodiments, the vessel may be filled by the sample handling system. Inembodiments, the cap may be placed on the vessel by the sample handlingsystem following filling of the vessel. In embodiments, the cap may beremoved by the sample handling system; for example, in embodiments, thecap may be removed by the sample handling system prior to filling thevessel with sample solution.

A cap as shown in FIG. 7 may be effective to prevent loss of samplefluid during sonication, and to prevent spread of sample contents (byspillage, aerosolization, or other means) outside the vessel. In thisfigure, a vessel is shown held in a vessel holder, and a sonicator hornis shown in contact with a side wall of the vessel. Such a configurationis an operative configuration effective to disrupt cells within thesample solution, such as pathogen cells within the sample solution.

A schematic illustration of a device having a sonicator and otherfeatures as disclosed herein is provided in FIG. 8. The deviceillustrated by the figure has a sonicator with a sonicator horn, whichcan be made to contact a wall of a vessel (e.g., by motion of a movablesonicator mount, as indicated in FIGS. 6A, 6B, and 7). The vessel cancontain a sample solution, and is configured to be held by a vesselholder. The vessel shown in FIG. 8 has a vessel cap. A sample handlingsystem may be provided effective to transport a biological sample, or aportion thereof, and reagents if applicable, to the vessel. As discussedherein, a sample handling system may also be configured to manipulate ormove a vessel, a vessel cap, or other article, within a housing of adevice. A device may have a detector, e.g., within the device housing asillustrated in the figure, such as a detector configured to detectpathogen-identifying materials released by sonication of a samplesolution. A device may further include other components for performingassays, detecting analytes, and collecting and communicating dataobtained from biological samples, and other actions. Such components mayinclude, e.g., components configured to perform assays, or to mixreagents, cameras, light sources, lenses, filters, temperature controldevices; temperature, optical, chemical or electronic sensors;mechanical components associated with such components, within the devicehousing as illustrated in the figure.

A sonicator may be used to deliver ultrasonic energy to a sample. Inembodiments, a sonicator may be used to deliver ultrasonic energy to asample in a vessel by contacting a vessel wall, and applying ultrasonicenergy to the wall effective to transfer ultrasonic energy to the samplewithin the vessel. The amount of energy provided by a sonicator maydepend on the ultrasonic frequency of the ultrasonic energy applied. Theamount of energy provided by a sonicator may depend on the amplitude ofthe ultrasonic energy. The amount of energy provided by a sonicator maydepend on the duration of the application of the ultrasonic energy. Theamount of energy provided by a sonicator may depend on the duty cycle ofthe application of ultrasonic energy (e.g., where the ultrasonic energyis not applied continuously for a duration, but is applied for a firsttime period, application of ultrasonic energy is ceased for rest timeperiod, and then ultrasonic energy is applied for a second time period,the combination of such periods may be termed a “duty cycle”; a dutycycle may be repeated to provide multiple periods during whichultrasonic energy is applied, separated by rest periods). The amount ofenergy provided by a sonicator may depend on the shape of thetime-varying ultrasonic energy applied (e.g., ultrasonic energy may beproduced by a transducer driven by square wave, sawtooth wave, sinewave, or other shaped signals).

In embodiments, a sonicator may be used to disrupt a cell, such as apathogen cell in a sample. In embodiments, a sonicator may be used tomix a solution; for emulsification of a solution or a mixture ofsolutions; for resuspension of a material, e.g., resuspension of asample following centrifugation of the sample; for aerosolization of aliquid; to heat a solution; to disperse a sample in, or into, asolution; to disintegrate a material; to de-gas a liquid; and for otheruses. The power requirements for one use of a sonicator may differ fromthe power requirements of another use of a sonicator. For example, thepower required to disrupt a cell in a solution may be greater than thepower required to mix a solution. The duration of power applied to asolution may differ depending on the use of the sonicator; for example,the duration of application of ultrasonic power used to heat a solutionwill depend on the initial temperature of the solution, and the desiredfinal temperature. The shape of the control signal sent to an ultrasonictransducer affects the power applied to a solution, and some shapes maybe more effective than others depending on the use of the sonicator.

A device as disclosed herein may comprise more than one sonicator. Asystem as disclosed herein may comprise more than one sonicator. In anembodiment as shown in FIG. 9, a single power supply may provide powerto drive multiple sonicators, where the power supply is connected via amultiplexer to the sonicators. In the example shown in FIG. 9, a single24 volt, 2 Amp (DC) power supply can output about 200 V to about 400 V(AC, at 40 Khz) via a single 6 channel probe power multiplexer effectiveto distribute six multiplexed output lines to six sonicators. Inembodiments, such a configuration may provide six devices, in a systemcomprising multiple devices (e.g., where each device may be termed a“bay” as indicated in FIG. 9). In embodiments, the output lines may bedetachable lines, configured to disengage a bay when desired or needed,and configured to allow reconnection to the power supply when desired orneeded (such connections may be termed “hot plugs” as indicated in thefigure). A multiplexer may be configured to control the sonicator pulseduration, or amplitude, or both, and so to control the duration ofultrasonic power transfer to a sample solution. The operation of themultiplexer selection may be according to a set pattern or frequency, ormay be controlled, for example, by a controller as shown in FIG. 1, ormay be controlled by other means. In embodiments of devices and systemsdisclosed herein, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more sonicators may beconfigured in this way, and may be controlled in this way.

In embodiments, a single sonicator may contact a plurality of vessels.In embodiments in which a single sonicator contacts a plurality ofvessels, the vessels may be disposed in an array of vessels. An array ofvessels may be a linear array, in which a sonicator may move along thearray and contact vessels sequentially. An array of vessels may becircular, or semicircular array, in which a sonicator rotates around anaxis effective to position the sonicator tip for contact with vesselsdisposed in such a circular or semicircular array. An array of vesselsmay comprise a combination of linear and curved arrays, may have anirregular shape, or vessesl may be disposed in any shaped array suitablefor contact with a sonicator tip.

In embodiments, multiple sonicators may contact a plurality of vessels,e.g., with a first sonicator contacting a first vessel, a secondsonicator contacting a second vessel, and so forth. In embodiments inwhich multiple sonicators contact a plurality of vessels, the vesselsmay be disposed in an array of vessels. In embodiments in which multiplesonicators contact a plurality of vessels, the sonicators may bedisposed in an array of sonicators. An array of sonicators, an array ofvessels, and both arrays, may be a linear array, may be a curved array,may be a combination of such arrays, may be an irregular array, and maybe any shaped array suitable for contact between a sonicator tip and avessel.

An embodiment of a vessel suitable for containing a sample solution forsonication is shown in several views in FIG. 10. A side view of avessel, with a flat wall surface facing outward, and the opening (forfilling the vessel) shown at the top is provided in FIG. 10A. A sideview with a flat wall surface facing rightward is shown in FIG. 10Bwhile FIG. 10C shows an angled view of the vessel. FIG. 10D shows across-sectional view of a vessel. The vessel of this embodiment has aflat side wall and a flat bottom; both the flat side wall and the flatbottom are configured to make effective contact with a tip portion of asonicator, such as a tip of a sonicator horn to provide for transfer ofultrasonic energy from the sonicator to a sample solution within thevessel. The wider portion at the top of the vessel includes surfaces andmating sockets. The mating sockets comprise recesses configured forengagement of a transport and/or force-providing member (e.g., a nozzleof a sample handling system) which a) allows transport of the vessel andb) provides a surface for provision of downward force to oppose upwardforce of a sonicator horn placed on a flat bottom surface of the vessel.Openings of the mating sockets are visible in this view, as is an innerridge within the internal chamber of the vessel. In embodiments, matingsockets may be configured to mate with a mechanical component configuredto transport a vessel, or to apply force to a vessel, or both. Inembodiments, such a mechanical component may be, or may comprise, asample handling system. In embodiments, such a mechanical component maycomprise a pipette, a nozzle, or other mechanical component.

FIG. 11 provides further embodiments of vessels suitable for containinga sample solution for sonication. Embodiments of vessels shown in FIG.11 have rounded bottoms, which are believed to be more suitable formixing, re-suspension, and other applications in which a sonicator isapplied to a wall of a vessel. FIGS. 11A, 11C, and 11D show embodimentsof tubular vessel with rounded bottoms. FIG. 11B shows an embodiment ofa conical vessel with a rounded bottom. FIG. 11C an embodiment of anelongated tubular vessel with a rounded bottom. FIG. 11D shows anembodiment of a wide tubular vessel with a rounded bottom. The vesselsshown in FIG. 11 are shown with caps; it will be understood that avessel may not be provided with a cap. In embodiments, caps may beremovable. In embodiments, caps may not be removable, but may bepiercable effective to fill a vessel without removing the cap. Inembodiments, caps may not be removable, but may comprise a passage forfilling or dispensing.

FIG. 12 provides yet further embodiments of vessels suitable forcontaining a sample solution for sonication. FIG. 12A shows anembodiment of a tubular vessel with a rounded bottom and a tapered(e.g., partially conical-shaped cap). A cap as shown in FIG. 12A mayform a tight seal with the lip of the vessel when pressed downwardly,due to its partially conical shape. A cap as shown in FIG. 12A mayprotrude into the interior of the vessel, or in embodiments, mayprotrude into the vessel only a small amount, or in embodiments, may notprotrude into the vessel. FIG. 12B shows an embodiment of a conicalvessel with a rounded bottom having flat side surfaces configured toengage with a sonicator tip. As indicated by the example of theembodiments of FIG. 11B and FIG. 12B, a conical vessel may have one,two, three or more flat surfaces configured for contact with asonicator. In embodiments, a conical vessel may have no such flatsurfaces, but a sonicator tip may press against the outer wall of aconical vessel lacking such surfaces as indicated in FIG. 11B and FIG.12B. FIG. 12C shows an embodiment of an elongated tubular vessel with arounded bottom and a protruding flat surface configured to engage with asonicator tip. It will be understood that, in embodiments, an elongatedtubular vessel with a rounded bottom may have two,. Three, or moreprotruding flat surface configured to engage with a sonicator tip. FIG.12D shows an embodiment of a wide tubular vessel with a rounded bottomhaving a cap connected to the vessel via cap linkage. Such a cap may beremovable, yet remain linked to the remainder of the vessel. A caplinkage may comprise a hinge, a tab, a thread, a perforated tab, or anyelement effective to connect the cap with the vessel body and allow theopening and closing of the vessel by movement of the cap.

As shown in FIG. 13, a vessel having a flat bottom may be contacted asillustrated by a tip of a sonicator. Such contact is effective totransfer ultrasonic energy to the wall of the vessel and thereby to asample solution contained within the vessel, effective to disrupt cellsin the sample solution. In embodiments, a sonicator tip may contact awall of a vessel, such as a lower wall as illustrated in FIG. 13, whilethe vessel is held in a vessel holder. In embodiments, a vessel held ina vessel holder may be in contact with no other components that providerestraint or retaining forces. For example, in embodiments, a sonicatortip may contact a wall of a vessel, such as a lower wall as illustratedin FIG. 13, while the vessel is held in a vessel holder without contactof a nozzle with a mating socket.

In embodiments, functional contact between the vessel and the sonicatormay be aided or improved by application of force (as illustrated by thedownward arrow in the figure) urging the vessel onto the tip of thesonicator horn, improving functional contact and improving energytransfer from the sonicator to the sample solution and cells within it.Force urging contact between the sonicator tip and the vessel bottom maybe provided by a spring, e.g., a spring as shown in the figure. Inembodiments, a nozzle of a sample handling system, or two nozzles of asample handling system, may engage with one or both mating sockets, andapply downward force effective to urge the base of the vessel onto thesonicator tip to improve contact between the vessel and the sonicatortip. In further embodiments, where one or two nozzles of a samplehandling system engage with one or both mating sockets, and applydownward force effective to urge the base of the vessel onto thesonicator tip, such application of force in conjunction with thepresence of the spring shown in FIG. 13 may improve the contact, orimprove control of the amount or effect of the applied force. The actionand function of the spring shown in FIG. 13 is to urge the sonicator andvessel together. This action is opposite to that of the springs shown inFIGS. 6A, 6B, and 7, which act to urge the sonicator and vessel apartfrom each other.

Thus, in embodiments, force urging contact between a sonicator tip and avessel wall may be provided by one or more of a solenoid, a spring, asample handling system, or other means.

Sonication is effective to disrupt cell membranes. Sonication may beused to release pathogen-identifying material into a sample solutioneffective to assay the sample, to detect the presence of pathogens, toidentify pathogens present in the solution, and to measure the amount ofpathogens present in the solution. Pathogens tested using devices withsonicators as disclosed herein included E. coli 884, S. pneumonia 3508,and Adenovirus 1.

Since nucleic acids are enclosed by cell or viral membranes, detectionof target pathogens demonstrates that the sonication has disrupted thesemembranes and made the pathogen-identifying nucleic acids available forassay. As shown in FIG. 14, pathogens were detected following sonicationusing quantitative polymerase chain reaction (qPCR). qPCR assays detecttarget nucleic acids indicative of the target pathogen; repeated cyclesdouble the number of copies of the target (if present); this process istermed amplification. Other detection methods may also be used,including other PCR methods known in the art, other nucleic acid assaysknown in the art, ELISA assays, other antibody-based assays,hemagglutinin assays (e.g., for influenza), and other assays. Thehorizontal axis of FIG. 14 represents the number of cycles while thevertical axis (in relative light units) represents the numbers of copiesof the target nucleic acid sequence indicative of the target pathogen.The horizontal line near the bottom of the figure (labeled “SYBR503.299”) indicates the lower limit for detection of pathogen nucleicacids. The cycle number at which a trace passes this threshold is the“cycle threshold” or “Ct” number; a target is considered detected whenthe results pass the threshold. A control (the traces at the far-rightof the figure, labeled “VialTweeter”) is shown, in whichpathogen-containing solutions in polypropylene containers mounted inwells of a block connected to an ultrasonic generator were subjected tosonication). The other traces result from experiments in which asonicator tip contacted walls of vessels holding pathogen-containingsolutions. As shown in the figure, nucleic acids from target pathogenswere detectable after about 25 cycles. Thus, sonication as disclosedherein may be effective to disrupt pathogens for use in the detection,identification, and measurement of pathogens in a sample.

While the above is a complete description of the preferred embodiment asdescribed herein, it is possible to use various alternatives,modifications and equivalents. Therefore, the scope of the presentinvention should be determined not with reference to the abovedescription but should, instead, be determined with reference to theappended claims, along with their full scope of equivalents. Anyfeature, whether preferred or not, may be combined with any otherfeature, whether preferred or not. The appended claims are not to beinterpreted as including means-plus-function limitations, unless such alimitation is explicitly recited in a given claim using the phrase“means for.” It should be understood that as used in the descriptionherein and throughout the claims that follow, the meaning of “a,” “an,”and “the” includes plural reference unless the context clearly dictatesotherwise. Also, as used in the description herein and throughout theclaims that follow, the meaning of “in” includes “in” and “on” unlessthe context clearly dictates otherwise. Finally, as used in thedescription herein and throughout the claims that follow, the meaningsof “and” and “or” include both the conjunctive and disjunctive and maybe used interchangeably unless the context expressly dictates otherwise.Thus, in contexts where the terms “and” or “or” are used, usage of suchconjunctions do not exclude an “and/or” meaning unless the contextexpressly dictates otherwise.

This document contains material subject to copyright protection. Thecopyright owner (Applicant herein) has no objection to the facsimilereproduction by anyone of the patent document or the patent disclosure,as they appear in the US Patent and Trademark Office patent file orrecords, but otherwise reserves all copyright rights whatsoever. Thefollowing notice shall apply: Copyright 2013 Theranos, Inc.

1-20. (canceled)
 21. A device configured to assay a sample for presenceof pathogen-identifying material, said device comprising: a sonicator; adetector, a sample handling system, a vessel holder configured to hold avessel, and a device to urge the sonicator apart from the vessel;wherein said vessel holder has a port to allow a sonicator tip of thesonicator to extend into the vessel holder and contact the vessel,wherein the vessel holder and the sonicator tip are movable relative toeach other.
 22. The device of claim 21, wherein said sonicator tip isconfigured to contact a vessel wall effective to transfer ultrasonicenergy from said sonicator to said vessel wall upon operation of saidsonicator.
 23. The device of claim 21, wherein said sonicator tip isconfigured to contact a vessel wall effective to transfer ultrasonicenergy from said sonicator to said vessel wall upon operation of saidsonicator, and optionally wherein the device is configured to applyforce to a vessel while applying a sonicator tip to a wall of a vessel.24. The device of claim 21, wherein said detector comprises an opticaldetector, and said device further comprises a communication assemblyconfigured to communicate with a user, a device, a laboratory, anetwork, or the cloud.
 25. A method of detecting the presence ofpathogen-identifying material in a biological sample, comprising:contacting said biological sample with device of claim 1; and detectingthe presence of a pathogen-identifying material in said sample.
 26. Themethod of claim 25, wherein said detecting comprises optical detection.27. The method of claim 25, wherein said biological sample comprises asample selected from blood, urine, sputum, tears, material from a nasalswab, material from a throat swab, material from a cheek swab, andanother bodily fluid, excretion, secretion, and tissue obtained from asubject.
 28. The device of claim 21 wherein said sonicator is configuredto contact an external face of said vessel effective to disrupt a cellin a sample within said vessel.
 29. The device of claim 21, wherein saiddevice is configured to perform an assay on a sample when said sample isheld in said vessel held by said vessel holder, said assay comprising anassay for pathogen-identifying material in the sample.
 30. The device ofclaim 21 wherein the vessel has a portion that is flat vessel side walland another portion with a curved side wall.
 31. The device of claim 28,wherein said detector comprises an optical detector and the devicefurther comprises a communication assembly configured to communicatewith a user, a device, a laboratory, a network, or the cloud.
 32. Theautomated assay device of claim 29, wherein said assay forpathogen-identifying material comprises an assay selected from an assayfor the detection of pathogen-identifying material in a sample; an assayfor identification of pathogen-identifying material in a sample; and anassay for measurement of an amount of pathogen-identifying material in asample, wherein said assay optionally comprises an isothermal assay. 33.The automated assay device of claim 28, wherein said biological samplecomprises a sample selected from blood, urine, sputum, tears, materialfrom a nasal swab, material from a throat swab, material from a cheekswab, and another bodily fluid, excretion, secretion, and tissueobtained from a subject.
 34. A system comprising: an automated assaydevice said automated assay device comprising a vessel holder, asonicator having a sonicator tip; a vessel, wherein said vesselcomprises a vessel wall having an external face, said external facecomprising a sonicator-contacting portion, wherein saidsonicator-contacting portion complementary to a portion of saidsonicator tip, and a device for urging the vessel holder and thesonicator tip apart; wherein said vessel holder having a port in a sidewall of the vessel holder to allow a sonicator tip of the sonicator toextend into the vessel holder and contact the sonicator-contactingportion, wherein the vessel holder and the sonicator tip are movablerelative to each other to bring said sonicator-contacting portion of thevessel into contact with the sonicator tip.
 35. The system of claim 34,wherein said sonicator-contacting portion of said vessel comprises aflat area of a side wall of the vessel.